########################################################################### # # File: mmcif_std.dic # Date: Tue Mar 8 05:54:42 EST 2005 # # Created from files in CVS module dict-mmcif_std.dic unless noted: # mmcif_std-header.dic # mmcif_std-data.dic # mmcif_std-def-1.dic # mmcif_std-def-2.dic # ########################################################################### ########################################################################### # # File: mmcif_std-header.dic # # mmCIF Data Dictionary # # This data dictionary contains the standard mmCIF data definitions. # # Header Section # # ########################################################################### ############################################################################## # # # Macromolecular CIF Dictionary # # # # Paula Fitzgerald, Helen Berman, Phil Bourne, Brian McMahon, # # Keith Watenpaugh, John Westbrook # # and many other contributors # # # # # # # # The review and extension process on this dictionary is is being # # administered through a discussion on a the mmCIF List Server being # # run out of Rutgers University. # # # # To subscribe to the mmCIF List Server, send a one line message # # containing the text: # # # # subscribe mmciflist Your Name # # # # to the email address: # # # # requests@ndbserver.rutgers.edu # # # # To post to the list, send messages to the email address: # # # # mmciflist@ndbserver.rutgers.edu # # # # Please use the list server for all questions, comments, and # # corrections that you may have concerning the draft dictionary. # # # # Should you have a question that you do not feel is appropriate # # for posting to the list, please feel free to contact one of # # Co-chairs of the IUCr mmCIF dictionary maintenance working group: # # # # Paula Fitzgerald # # Merck Research Laboratories # # P.O. Box 2000, Ry50-105 # # Rahway, New Jersey, 07065 USA (paula_fitzgerald@merck.com). # # # # Helen M. Berman # # Department of Chemistry # # Rutgers the State University of New Jersey # # 610 Taylor Road # # Piscataway, New Jersey 08854-8087 USA (berman@rcsb.rutgers.edu) # # # # Questions concerning the process of review and approval of the # # CIF dictionaries by the International Union of Crystallography # # should be addressed to the Coordinating Secretary of the IUCr # # Committee for the Maintenance of the CIF Standard, Brian McMahon, # # IUCr, 5 Abbey Square, Chester CH1 2HU, England (bm@iucr.org). # # # # Copyright 2005 International Union of Crystallography # ############################################################################## # # # This dictionary is compliant with DDL v2.1. As such, it looks # # substantially different from the previously approved and released # # versions of the CIF core dictionary. This dictionary contains all # # data items that were present in the CIF core dictionary. To those # # data items have been added the large number of data items needed to # # describe the macromolecular crystallographic experiment and its # # results. # # # ############################################################################## data_mmcif_std.dic _datablock.id mmcif_std.dic _datablock.description ; This data block holds the mmCIF data dictionary, standard definitions. ; _dictionary.title mmcif_std.dic _dictionary.version 2.0.09 _dictionary.datablock_id mmcif_std.dic ######################## ## DICTIONARY_HISTORY ## ######################## loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 0.1.1 1993-02-11 ; Highlighted all notes with # %%%%% surrounds. ; 0.1.2 1993-02-11 ; Started moving examples to *_appendix data items. ; 0.1.3 1993-02-11 ; Started moving core data names to the *_appendix data items ; 0.1.4 1993-02-11 ; Added example for _symmetry_ ; 0.1.5 1993-03-24 ; Finished moving examples to *_appendix data items ; 0.1.6 1993-03-24 ; Dealt with many issues raised by SR Hall. Some were merely typographical. Changed temp to B_iso Changed occ to occupancy Changed special_details to details. Changed asl to label everywhere. Shuffled data names in _struct_conf_ and _struct_conn_ ; 0.1.7 1993-03-24 ; Tested for Cyclops compliance - most problems are names that are too long. Changed crystal_preparation to crystal_prep Changed d_resolution to d_res Many other such changes ; 0.1.8 1993-03-25 ; Still testing for Cyclops compliance - reveal many additional syntax problems Also verified with new tool by RG Ball - still more errors fixed Dealt with issue raised by PE Bourne - amongst changes Rewrote _database_ section completely Changed _audit_contact_author_ to _audit_contact_author_name _audit_contact_author_address ; 0.1.9 1993-03-26 ; Removed _struct_topol_ section until it gets straightened out ; 0.1.10 1993-03-28 ; Filled in examples for several data categories ; 0.1.11 1993-04-03 ; Syntax checked using tools of Peter Murray-Rust - many problems fixed ; 0.1.12 1993-04-06 ; More syntax problems fixed a la Peter Murray-Rust ; 0.1.13 1993-04-07 ; Introduced _exptl_crystal_grow_ data names ; 0.1.14 1993-04-07 ; Experiment with refers_to, category and part_of_key in entity_conn_atom_ and entity_conn_bond_ sections. Discovered horror show with nonconcurrent versions on different computers - not yet resolved. ; 0.1.15 1993-05-09 ; Reconciled nonconcurrent versions Removed trailing blanks Made corrections based on email suggestions from P. Bourne ; 0.1.16 1993-05-10 ; Made corrections based on written comments from K. Watenpaugh Made corrections/additions based on discussions at Rutgers ; 0.1.17 1993-05-11 ; Changed _atom_site_label_component_? to new nomenclature Introduced category DDL throughout Introduced refers_to DDL throughout Introduced part_of_key DDL throughout Mandated that _list must be in each data definition Standardized 'need not be unique' statements Standardized example headers ; 1.1.18 1993-05-12 ; Looped out authors and editors in citation list Verified with RGB tools Some style consistency imposed Fleshed out category definitions and imposed style Updated "sets of data item" at beginning of document Checked alphabetical order of data names - moved id's ; 0.2.1 1993-05-13 ; Major rethinking of _entity_ data based following discussions of 1993-05-10 meeting ; 0.2.2 1993-05-18 ; Style consistency and proof reading changes throughout Make page numbers general to articles and chapters in citation Added *_method to all phasing categories Looped out keywords from _struct_site_ list Added _atom_site_label_ definitions as per H. Berman Added _struct_biol_view_ and struct_site_view_ items as per P. Bourne Added _atom_sites_alt_ data items to formally handle alternative conformations Verified with Cyclops and RGB tools ; 0.2.3 1993-05-19 ; Fixed based on problems unearthed by Peter Murray-Rust and Brian McMahon ; 0.2.4 1993-05-20 ; DDL adjustment from down under ):-(> ; 0.2.5 1993-05-20 ; A general merging of updates from PMR, BMcM and SRH Fixed typographical and stylistic problems a la BMcM ; 0.2.6 1993-06-02 ; Fixed _atom_site_ example (_entity_poly_seq_num) Removed _list_link_parent from _entity_mon_atom_atom_id a _entity_nonp_atom_atom_id Added real APS coordinates to _atom_site_ example Rewrote _atom_sites_footnote_ example ; 0.2.7 1993-08-01 ; Redesigned phasing_MIR definitions ; 0.2.8 1993-08-03 ; More work on phasing_MIR Created phasing_MIR_der and phasing_MIR_der_shell categories ; 0.3.1 1993-08-08 ; Began implementing DDL v0.7 ; 0.3.2 1993-08-11 ; Cleaning up of stray notes ; 0.3.3 1993-08-12 ; Syntax and consistency checks - SRH Added _type of null for appendix items. ; 0.3.4 1993-09-01 ; Added _struct_conn_ptnr1_label_alt_id and _struct_conn_ptnr2_label_alt_id Corrected definitions for _struct_conn_ptnr2_ items Added _struct_site_gen_label_alt_id Fixed Cullis reference in _phasing_MIR_der_shell_R_Cullis Change _database_PDB_rev_ example to _loop construction Added _PDB_remark category (data items _PDB_remark_num and _PDB_remark_text) Added 'obsolete' to enumeration list for _database_PDB_rev_status Added _database_PDB_rev_replaces data item ; 0.3.5 1993-09-08 ; Added missing _diffrn_orient_matrix_UB_33 (in appendix) Added missing _phasing_MIR_der_shell_der_id to appropriate example ; 0.3.6 1993-10-10 ; Changed *_appendix to *_[mm] throughout Removed 'Need example here' from _chemical_[mm] Removed 'Need example here' from _chemical_conn_atom_[mm] Removed 'Need example here' from _chemical_conn_bond_[mm] Moved _PDB to end of all relevant data names (except _[mm]) Added _database_rev_record_details_PDB data name Changed _refine_occupancy_limit_high to _refine_occupancy_max Changed _refine_occupancy_limit_low to _refine_occupancy_min Changed _refine_B_iso_limit_high to _refine_B_iso_max Changed _refine_B_iso_limit_low to _refine_B_iso_min Changed all definitions and examples in _refine_iso_B_ category to _refine_B_iso_ equivalents ; 0.3.7 1993-11-16 ; Changed form of dates in _update_history to CIF style Changed ? to . in examples, where appropriate Added _example_detail to _refine_ls_restr_type Expanded definition of _refine_ls_restr_type ; 0.3.8 1993-11-30 ; Moved _audit_author_, _citation_ categories to CIF core Definitions and small-molecule examples removed from *_[mm] sections that don't extend core categories - BMcM ; 0.3.9 1993-12-02 ; Deleted section summarizing categories - PMDF Returned definitions for most *_[mm] sections - PMDF Added _list and _list_level to global - PMDF Changed form of dates from yy-mm-dd to yyyy-mm-dd - PMDF Checked lists of data items in core, fixing some problems with missing names and alphabetization - PMDF Resorted some categories to correct alphabetization - PMDF Changed form and definitions of _database_remark_num_PDB and _database_remark_text_PDB - PMDF Added data item _database_rev_replaced_by_PDB - PMDF Reordered data items in _citation example - PMDF Added data item _exptl_crystal_density_%_sol - PMDF ; 0.3.10 1993-12-15 ; Various changes following suggestions from BMcM Refined definition of _atoms_site_label_atom_id - PMDF Removed _atom_sites_fract_tran (moved to core) - PMDF Changed _diffrn_crystal_physical_device to _diffrn_crystal_support - PMDF Changed _diffrn_measure_device_part to _diffrn_measure_device_specific - PMDF Changed _diffrn_rad_detector_part to _diffrn_rad_detector_specific - PMDF Changed _diffrn_rad_source_part to _diffrn_rad_source_specific - PMDF Changed *_par1* and *_par2* to *_ptnr* in _struct_conn* - PMDF Fixed several occurrences of \&A instead of \%A - PMDF ; 0.3.11 1993-12-22 ; Made a number of fixes relayed by PEB from MS AND RH _type of _atom_site_footnote_id (numb->char) - PMDF _type of _database_rev_record_rev_num_PDB (char->numb) - PMDF _type of _phasing_MIR_der_number_of_sites (char->numb) - PMDF _atom_sites_fract_tran_matrx to _matrix - PMDF _type of _phasing_MIR_site_details (numb->char) - PMDF _example of _struct_conf_type_reference - PMDF ; 0.3.12 1993-12-23 ; Broke out examples from intro sections to loop_ _item_examples.case _example_detail construction - BMcM ; 0.3.13 1994-01-13 ; Rationalization of categories between mm and core dicts - BMcM Deleted _diffrn_crystal_environment (same as core _diffrn_ambient_environment) and moved other _diffrn_crystal items to core - BMcM Fixed typos, removed hyphenation ("be kind to ciftex") - BMcM Some re-alphabetization - BMcM ; 0.3.14 1994-01-26 ; Lots more re-alphabetization - PMDF Changed non_s to nstd throughout - PMDF Changed nonp to npol throughout - PMDF Removed all multiple spaces - PMDF Fixed a couple of alignment problems - PMDF ; 0.4.1 1994-02-04 ; Major modifications of _entity_ subcategories - PMDF Added angles, planes, torsion angles and chiral centers to _entity_mon_ and _entity_npol_ Added many missing definitions Added many missing examples ; 0.4.2 1994-02-25 ; Corrected spelling errors found by BMcM - PMDF ; 0.4.3 1994-03-28 ; Various changes following suggestions by IDB - PMDF Changed _entity_mon_angle_value to _entity_mon_angle_value_angle in example Changed _entity_npol_bond_value to _entity_npol_bond_value_dist Changed nonp to npol in _entity_npol_tor_value category Reworded angle _enumeration_details in _refine_ls_restr_type Reworded definitions in _struct_asym_[mm] and _struct_biol_[mm] Reworded definitions of _struct_conn_symmetry_* _struct_site_gen_symmetry _struct_biol_gen_symmetry Split _struct_conn_symmetry_* into _struct_conn_ptnr1_symmetry and _struct_conn_ptnr2_symmetry Split _struct_conn_role_* into _struct_conn_ptnr1_role and _struct_conn_ptnr2_role Removed _list_link_child from _struct_conn_conn_type_id Added _list_link_child to _struct_conn_type_id ; 0.5.1 1994-10-10 ; Implementation of Treaty of Brussels - PMDF Merged CIF core dated 1994-03-01 (from BMcM) with mm dictionary dated 1994-05-20. The history records for the core dictionary are included here to identify the version of the core that was merged: _dictionary_name cifdic.c94 _dictionary_version 2.0 _dictionary_update 1994-03-01 _dictionary_history 1991-05-27 Created from CIF Dictionary text. SRH 1991-05-30 Validated with CYCLOPS & CIF ms. SRH 1991-06-03 Adjustments to some definitions. SRH 1991-06-06 Adjustments a la B. McMahon. SRH 1991-06-18 Additions & some redefinitions. SRH 1991-07-04 Corrected 90:0 in *_detect_slit_. SRH 1991-09-20 Additions & some redefinitions. SRH 1991-09-20 Final published version. IUCr 1991-11-12 Add _diffrn_ambient_environment. SRH 1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH 1993-02-23 Apply global_ and 'unknown' -> '?' SRH 1993-03-05 Changes resulting from MM dictionary. SRH 1993-05-20 Changes arising from new DDL commands. SRH 1993-08-05 Additional fine tuning pre-Beijing. SRH 1993-12-22 Introductory sections added to categories. BMcM 1993-12-22 Additional categories from mm work: _audit_author, _citation, _atom_sites_fract_tran_matrix. BMcM 1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM 1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM 1994-03-01 Add 'atom_site_aniso_ratio'. BMcM -------------- Removed all mm sections that enumeration items present in core but not present in mm dictionary. Fixed errors with missing trailing _'s in some category headers Also unbalanced ##'s in same place Removed "End of Example" statement everywhere Standardized syntax for missing examples Standardized syntax and style for category _definition data items. Added a bunch of ending dashed lines where they were missing. Merged [] and [mm] category explanation sections. Made HIV example always example 1, moved examples from core (where they were different from the HIV example) to higher numbers. Changed data_ to save_ everywhere Changed _name to _item.name everywhere Added _item.mandatory_code everywhere Added save_ everywhere Moved _description to top of _save frame everywhere Changed _example to _item_examples.case everywhere Changed _example_detail to _item_examples.detail everywhere Changed _description to _item.description.description everywhere Removed _list yes everywhere Removed _list_reference everywhere Changed _enumeration_range to enumeration_limit.minimum and enumeration_limit.maximum everywhere ; 0.5.4 1994-11-14 ; Implementation of DDL 2.0.7 dictionary wide - PMDF Changed _enumeration to _enumeration.code Changed _enumeration_detail to _enumeration.code_detail Changed _enumeration_default to _enumeration_default.code Put .'s in item names (incomplete) Moved _PDB back to appropriate place in item names in the _database_remark_PDB_ and _database_rev_PDB_ and _database_rev_record_PDB_ categories Changed database_rev_PDB to database_PDB_rev Changed database_remark_PDB to database_PDB_remark Changed database_rev_record_PDB to database_PDB_rev_record Changed category items from item to category Began getting rid of *_whatever construction in category and item descriptions ; 0.5.5 1994-11-15 ; Implementation of DDL 2.0.7 dictionary wide - PMDF Finished putting .'s in itme names Changed _diffrn_measure_ to _diffrn_measurement. Changed _diffrn_rad_ to _diffrn_radiation. Implemented category and ID pointers for entity category. Found all sorts of errors while doing this, and attempted to fix them consistently. Did not remove child data Items, even though they don't have to be specified - they should help keep all of this straight during the transition. Some silly reformatting to ensure that data values always have the first alphabetic character in column 33. More silly reformatting to put each example in an example loop on a separate line. ; 0.6.1 1994-11-21 ; Changes (JDW): + Converted dictionary and dictionary_history categories. Incorporated core dictionary history list into the new history list in the revision 0.5.1 where the dictionary merger is firsted discussed. ; 0.6.2 1994-11-28 ; Changes (PMDF): + Made loop_ _item.name data items into separate data items This involved rewriting the definitions of most of them. In doing so I continued to eliminate the a.b_* construction. Added unit type of degrees. Added unit type of minutes. Added unit type of electrons. ; 0.6.3 1994-11-30 ; Changes (PMDF): + Finished conversion of units data items Added a number of unit types to the table Conversation table still need to be fleshed out Removed _list_mandatory and changed _item_mandatory.code to yes for those data items ; 0.6.4 1994-12-01 ; Changes (PMDF): + Began conversion of _list_link_parent items to appropriate new DDL relationships ; 0.6.5 1994-12-02 ; Changes (PMDF): + Began implementation of new scheme for relationships in the entity category All entities will be treated as polymers - non-polymers will have a number of monomers of 1 All data items in ENTITY_NPOL categories are eliminated All data items in ENTITY_POLY category are moved to ENTITY ; 0.6.6 1994-12-06 ; Changes (PMDF): + Finished conversion of _list_link_parent items to appropriate new DDL relationships Filled out category_key.id items in each category Had to add diffrn_refln.id item, as cannot use h k l in that category (perfectly valid to measure same reflection more than once). Used _diffrn_standard_refln.code in that category - this may cause a problem with old files, as example file did not give this data item Moved _entity_poly items back to _entity category Moved _entity_poly.formula_weight to entity.formula_weight Used _exptl_crystal.id in that category - this may cause a problem with old files, as example file did not give this data item Added _exptl_crystal_grow.crystal_id in that category Added _symmetry_equiv.id in that category - this may cause a problem with old files, as this is a new data item ; 0.6.7 1994-12-07 ; Changes (PMDF): + Created DATABASE_NEW category to solve logical problems with old DATABASE category. Need to think some more about how old data items are handled. Added aliases for remaining c91 data items Changed geom_angle to geom_angle.value (aliased to original name) Changed geom_torsion to geom_torsion.value (aliased to original name) Returned ATOM_SITE items taken out during ATOM_SITE_MM transition ; 0.6.8 1994-12-08 ; Changes (PMDF): + Created ATOM_SITE_ANISOTROP category to provide for ability to have anisotropic data is a separate loop, if desired. Checked and fixed a bunch of style things Added item_units.code of degrees in data items with degrees in the description but not in the ddl Added item_units.code of kelvin in data items with kelvin in the description but not in the ddl (and added 'in degrees kelvin' to the description of those with item_units.code of kelvin but no corresponding phrase in the description) Added item_units.code of microseconds to _diffrn_radiation.detector_dtime (added to units list at same time) Added 'in minutes' to description of _diffrn_refln.elapsed_time Added 'in kilopascals' to to the description of those with item_units.code of kilopascals but no corresponding phrase in the description Added BLOCK category Added appropriate pointers (in category key, and with a data item pointing to _data_block.id) in all categories that needed them ; 0.6.9 1994-12-09 ; Changes (PMDF): + Added _esd data items where needed Rationalized descriptions for all of the coordinate data items ; 0.6.10 1994-12-13 ; Changes (PMDF): + Established check-list for unfinished tasks and began dealing with them Added enumeration limits of 0 and 1 and enumeration default of 1.0 to occupancy data items Left heavy-atom maximum with an enumeration of ? Added enumeration default of 1_555 to all _symmetry data items where it was missing Changed 'connect type' to 'interaction' in _struct_conn_type data items. Filled out sub_category ddl items for cartesian coordinates, fractional coordinates, cartesian coordinates esds, and Miller indices. ; 0.6.11 1994-12-14 ; Changes (PMDF): + Fixed R-Kraut reference Changed _reflns_shell.possible_&_all to _reflns_shell.percent_possible_all Changed _reflns_shell.possible_&_obs to _reflns_shell.percent_possible_obs Changed _exptl_crystal.density_%_sol to _exptl_crystal.density_percent_sol Included full formula for this calculation in description Changed _refine_ls_restr.model _refine_ls_restr.dev_ideal Changed _refine_ls_restr.target _refine_ls_restr.dev_ideal_target Improved wording of all definitions in REFINE_LS_RESTR Explained sums in _reflns_shell.Rmerge_I_obs and related data items ; 0.6.12 1994-12-15 ; Changes (PMDF): + Changed _enumeration_default.code to _item_default.value Changed _enumeration_default.value to _item_default.value Changed _enumeration.code to _item_enumeration.value Changed _enumeration.detail to _item_enumeration.detail Changed _enumeration.case to _item_enumeration.value Changed _enumeration_limit.maximum to _item_range.maximum Changed _enumeration_limit.minimum to _item_range.minimum Checked that matrix were properly labeled as either rw_rowwise or just plan rowwise. Reworded matrix descriptions for consistency. Got rid of the last of the a.b_* constructions in descriptions Added cell_length, cell_length_esd, cell_angle and cell_angle_esd subcategories Changed special_details to details for core items - original names retained in aliases Added atom_site.id Added mm_atom_site_label subcategory Commented out _atom_site.label_component until it can be dealt with properly Changed 'SIF' to 'data block' in a number of descriptions. ; 0.6.13 1994-12-16 ; Changes (PMDF): + Added data item _refln.R_free_status Added data item _reflns.R_free_details Changed _refine_ls_shell.reflns to refine_ls_shell.number_obs Added _refine_ls_shell.number_R_free Added _refine_ls_shell.number_all Added _refine_ls_shell.R_factor_R_free Added _refine_ls_shell.wR_factor_R_free Tidied up the count and R-factor descriptions in REFINE_LS_SHELL Added appropriate item_related names to the R-factors in REFINE_LS_SHELL Changed 'count' to 'number' in several data names Changed _reflns.number_total to _reflns.number_all Changed _reflns.number_observed to _reflns.number.obs Added _refine.ls_R_factor_R_free Added _refine.ls_wR_factor_R_free Edited descriptions of the other R-factor data items in the REFINE category to conform to the style in REFINE_LS_SHELL Re-alphabetized the things I changed yesterday from special_details to details - I had forgotten to do that yesterday ; 0.6.14 1994-12-19 ; Changes (PMDF): + Changed refine.ls_number_reflns to refine.ls_number_reflns_obs Added refine.ls_number_reflns_all Added refine.ls_number_reflns_R_free Changed _refln.observed_status to refln.status Expanded enumeration list to include resolution limits and R-free flag Rewrote definition Eliminated refln.R_free_status Changed _refine_ls_shell.number_all to _refine_ls_shell.number_reflns_all Changed _refine_ls_shell.number_obs to _refine_ls_shell.number_reflns_obs Changed _refine_ls_shell.number_R_free to _refine_ls_shell.number_reflns_R_free Added PHASING category Filled in and reformatted units conversion table ; 0.7.1 1994-12-19 ; Changes (JDW): + First pass through SIFLIB checking tools. Corrected syntax errors and missing parent references. ; 0.7.2 1994-12-20 ; Changes (PMDF): + Merged JDW changes with version 0.6.12 Changed _item_type.code of numb to either int or float Changed _item_description.description to category.description where appropriate Fixed a bunch of pure syntax errors Removed 'refln_scale_group' from list of category groups. Changed _refln_scale_group_code to _refln.scale_group_code somewhere Changed REFLN_SCALE_GROUP_CODE to _refln.scale_group_code somewhere Reformatted CATEGORY_GROUP_LIST items to match style of other header categories Ensures that all _category data items obey they rule of first alphabetic character is column 34 (most didn't before this check) Removed _item_related stuff from _atom_site.aniso_U[1][1] (at the rest) data items, and added wording to description that these items are only there for compliance via the alias (but left in the one _item_related thing that made the matrix element data item alternate exclusive to the full matrix data item Added language about compliance to _atom_sites.Cartn_tran_matrix Added language about compliance to _diffrn_orient_matrix.UB Added language about compliance to _diffrn_reflns.transf_matrix Removed matrix element data items for _atom_sites.fract_tran_matrix - this wasn't in c91 and so doesn't need aliasing ; 0.7.3 1994-12-22 ; Changes (PMDF): + Fixed things turned up by JDW checking of 0.7.2 Couple of small typos Added angstroms_cubed to units list and conversion tables Added _phasing_MIR_site.atom_type_symbol and added this reference to the table until _atom_type.symbol Added _entity_mon_atom.substruct_code Began adding STRUCT_MON_PROT, but this is not yet complete ; 0.7.4 1995-01-12 ; Changes (PMDF): + Finished working on STRUCT_MON_PROT category Added STRUCT_MON_DETAILS category Added STRUCT_MON_PROT_CIS category Added STRUCT_NCS_ENS category Added STRUCT_NCS_ENS_OPER category Added STRUCT_NCS_DOM category Added STRUCT_NCS_DOM_GEN category Added equations to definitions of _phasing_MIR_der_shell.fom and _phasing_MIR_shell.fom Added REFINE_HIST category ; 0.7.5 1995-01-13 ; Changes (PMDF): + Provided for sequence microheterogeneity by making _entity_poly_seq.mon_id part of the category key and by adding the data item _entity_poly_seq.hetero as a flag Added ENTITY_POLY_SEQ_DIF category - this meant adjusting some pointer in referenced data items. Added _entity_mon_atom.alt_atom_id. Added COMP_PROG category Removed non-c91 COMPUTING data items (phasing averaging, MAD, MIR and MR) ; 0.7.6 1995-01-17 ; Changes (PMDF): + Added ENTITY_SRC_NAT category Added ENTITY_SRC_GEN category Added ENTITY_NAM_COM category Added ENTITY_NAM_SYS category Added _entity.src_method data item Moved other entity data items to new categories as appropriate ; 0.7.7 1995-01-18 ; Changes (PMDF): + Added PHASING_MIR_REFLN category ; 0.7.8 1995-01-25 ; Changes (PMDF): + Added _entity_mon.type, _entity_mon.number_atoms_all, _entity_mon.number_atoms_nh, _entity_mon.one_letter_code Added _entity_mon_angle.value_angle_esd, _entity_mon_angle.value_dist_esd, _entity_mon_bond.value_dist_esd Added _entity_mon_atom.type_energy, but since this is intended to be a pointer to a category (_atom_type_energy) that doesn't exist yet, have left it commented out Added _entity_mon_chir.volume_three, _entity_mon_chir.volume_three_esd and _entity_mon_chir.volume_flag Added _entity_mon_plane.number_atoms_all, _entity_mon_plane.number_atoms_nh Added _entity_mon_chir.number_atoms_all, _entity_mon_chir.number_atoms_nh Added _entity_mon_chir_atom.dev Added _entity_mon_tor_value.angle_esd, _entity_mon_tor_value.dist_esd Added ENTITY_LINK category Added ENTITY_LINK_ANGLE category Added ENTITY_LINK_BOND category Changes (HB et al.): + Added STRUCT_MON_NUCL category Changes (PMDF): + Added label links from STRUCT_MON_NUCL to rest of dictionary Added label links from STRUCT_MON_PROT as well (forget them initially) ; 0.7.9 1995-01-30 ; Changes (PMDF): + Fixed syntax errors unearthed by checking of JW and PDB ; 0.7.10 1995-02-03 ; Changes (PMDF): + Removed loop_ construction from loop_ or order one, except not for category examples and not for parent/child loops Standardized style of yes/no enumeration lists Made style of all enumeration lists more standard (still not happy here) Standardized style of examples Standardized style of references in definitions Began standardizing style of equations in definitions ; 0.7.11 1995-02-07 ; Changes (PMDF): + Finished standardizing style of equations in definitions Moved ITEM_TYPE_LIST to bottom of dictionary Moved ITEM_UNITS_LIST to bottom of dictionary Moved ITEM_STRUCTURE_LIST to bottom of dictionary Moved DICTIONARY_HISTORY to bottom of dictionary (it will come back up to the top with version 1.0.0) Rewrote dictionary header comments to reflect this dictionary ; 0.7.12 1995-02-09 ; Changes (JDW): + Changed _atom_site.label_res_id to _atom_site.label_comp_id which is a child of _chem_comp.id. + Changed all children items named label_res_id to label_comp_id + Changed descriptions of many label_comp_id to reference correct parent item. (_atom_site.label_comp_id rather than comp_comp.id). + Changed ENTITY_MON to CHEM_COMP and removed polymer component specific terminology. + Changed ENTITY_LINK to CHEM_LINK and removed polymer component specific terminology. + Added data type for yyyy-mm-dd and applied this where appropriate. + Added chem_comp_group and chem_link_group to the category group list. + Added '_' prefix to all data item save frame names. ; 0.7.13 1995-04-20 ; Changes (PMDF): + Changed all matrices back to element by element representation. + Reworded definitions of B and U matrices to clarify alternate exclusive relationship + Changed 'miller' to 'Miller' in some definitions, but left it 'miller' in data values. + Changed 'CIF' to 'data bock' where appropriate. + Made changes according to notes from last Rutgers meeting. Mostly this is clearer wording of definitions. Made formal Ref: for scattering factors. Changed atom_site.description to atom_site.details Expanded definitions for the components of the atom site label. Added disclaimer to some records in ATOM_SITE and ATOM_SITES categories. Changed _atom_type.analytical_mass_% to _atom_type.analytical_mass_percent Expanded definition of AUDIT category Added separate esd data items to examples in CELL category Added real formula in definition of _cell.volume Moved disclaimer to the top in CHEMICAL categories Changed enumeration to example in _chem_comp.one_letter_code Changed _phasing_MIR_refln.F_sigma to _phasing_MIR_refln.F_meas_sigma and adjusted definition to style of other esd definitions. Added type condition esd to _phasing_MIR_refln.F_meas Changed refln.observed_status to refln.status in example Changed _refln.F_sigma to _refln.F_meas_sigma and adjusted definition to style of other esd definitions. Added type condition esd to _refln.F_meas ; 0.7.14 1995-05-03 ; Changes (PMDF): + Fixed definitions of _phasing_MIR_refln.index_k and _phasing_MIR_refln.index_l ; 0.7.15 1995-05-18 ; Changes (PMDF): + Added DDL linking data names that are value to the data names that are esds of those values Changed _geom_bond.distance to _geom_bond.dist and _geom_bond.distance_esd to _geom_bond.dist_esd Changed _geom_contact.distance to _geom_contact.dist and _geom_contact.distance_esd to _geom_contact.dist_esd Changed _cell_measurement.temperature to _cell_measurement.temp and _cell_measurement.temperature_esd to _cell_measurement.temp_esd Changed _diffrn.ambient_temperature to _diffrn.ambient_temp and _diffrn.ambient_temperature_esd to _diffrn.ambient_temp_esd ; 0.7.16 1995-05-18 ; Changes (PMDF): + Added _item.name DDL to those data items that didn't have it Wrote program to check that the added names were all correct Fixed problems that turned up (including one missing . in _diffrn_radiation_detector_details ; 0.7.17 1995-05-22 ; Changes (PMDF): + Added _phasing_MIR_refln.F_meas_au and _phasing_MIR_refln.F_meas_au_sigma and adjusted appropriate _item.related DDL Added _refln.F_meas_au and _refln.F_meas_au_sigma and adjusted as above Added _phasing_MIR_refln.F_calc_au and adjusted as above Added _refln.F_calc_au and adjusted as above Added _refln.A_calc_au and adjusted as above Added _refln.B_calc_au and adjusted as above Added _refln.A_meas_au and adjusted as above Added _refln.B_meas_au and adjusted as above Changed _item_related.function_code from 'replace' to 'alternate_exclusive' in database_2 data items Added _item_related DDL to appropriate _database data items ; 0.7.18 1995-07-20 ; Changes (JDW): + Added '_struct_biol_gen.symmetry' to the key on struct_biol_gen. + Changed category block to entry. + Added _dictionary.datablock_id + Replace publ_group and journal_group with category group named iucr_group + Added category group named pdb_group + Removed all the _atom_site.label references and repointed any references to this item to _atom_site.id. + Added optional atom identifiers to all of the GEOM categories. + Added translation vector to transformations in ATOM_SITES + Created subcategories for matrices and vectors + Moved _struct.keywords to a new category STRUCT_KEYWORDS + Added pointer to exptl_crystal.id as part of key in category EXPTL_CRYSTAL_GROW_COMP. + Restructured DATABASE_PDB_REMARK category + Changed alternate_exclusive to replaces and replacedby in DATABASE and DATABASE_2 + Restructured examples in _chem_comp.one_letter_code ... + Added data item _chem_comp.three_letter_code + Made atom_site.label_alt_id and its children an optional item + Changed item names _atom_sites.frac_tran_* _atom_site.frac_transf_* and _atom_sites.Cartn_tran_* _atom_site.Cartn_transf_* + Changed the key of ATOM_SITE_ANISOTROP to _atom_site_anisotrop.id + Added all of the GEOM category atom label items to their appropriate parent data items. + 'arbitrary' added to list of item_units_list.code's + Fixed conflicting mandatory codes... ; 0.7.19 1995-07-23 ; Changes (JDW & PMDF): + Minor corrections in sheet example and version update. + Removed illegal characters from data item names. Changed any "/" in data item names to "_over_". ; 0.7.20 1995-08-02 ; Changes (PMDF): + Enforced 80 character per line limit throughout. + Realphabetized _geom_angle.value and _geom_angle.value_esd. + Realphabetized _geom_torsion.value and _geom_torsion.value_esd. + Removed trailing blanks. + Fixed a couple of problems with missing terminal '. ; 0.7.21 1995-08-08 ; Changes (PMDF): + Added _citation_author.ordinal and updated examples to reflect this addition. + Changed _item.mandatory_code for _citation_author.name to 'yes'. + First pass at checking the dictionary for spelling - lots of little changes in lots of places. + Removed many occurrences of 'with with' in definitions. ; 0.7.22 1995-08-09 ; Changes (PMDF): + Added definitions for _chem_link_angle.link_id and _chem_link_bond.link_id + Straighted out spacing inconsistencies with _item.mandatory_code + Another quick pass at spell checking ; 0.7.23 1995-08-10 ; Changes (PMDF): + Changed _struct_sheet_gen.label_seq_id to _struct_site_gen.label_seq_id in _atom_site.label_seq_id tree + Removed duplicate entry of _phasing_MIR.entry_id in _entry.id tree + Removed alias in definitionof _refln.A_meas_au + Removed _item.category_id from _chem_link.type_comp_1 _chem_link.type_comp_2 _phasing_mad_clust.expt_id _phasing_mad_set.clust_id _phasing_mad_set.expt_id _phasing_mad_set.set_id _phasing_mad_ratio.expt_id _phasing_mad_ratio.clust_id _phasing_mad_ratio.wavelength_1 _phasing_mad_ratio.wavelength_2 + Removed _item_type.code from most of the above (it wasn't there in all of them). + Added _item.mandatory_code to _phasing_mir_der.der_set_id + Corrected _item.name for _phasing_mad_ratio.wavelength_2 ; 0.7.24 1995-08-21 ; Changes (PMDF): + Corrected category.id for data items in the DIFFRN_STANDARDS category + Corrected category.id for data items in the PHASING_MAD_EXPT category + Corrected category.id for selected data items in the PHASING_SET category + Corrected alias for _atom_site.thermal_displace_type + Introduced alias of _atom_site_aniso_label for _atom_site_anistrop.id + Introduced alias of _atom_site_aniso_type_symbol for _atom_site_anisotrop.type_symbol ; 0.7.25 1995-08-31 ; Changes (PMDF): + Eliminated duplicate line in _entry_id parent/child table + Changed the three occurrences of _item_type.code text to char _atom_sites_alt.details _atom_sites_alt_ens.details _database_PDB_remark.text + Fixed Klyne and Prelog reference in GEOM_TORSION category description + Added data item _chem_comp_chir.atom_config + Added hyphen in non-crystallographic in definition sof _struct_ncs_ens.point_group + Changed Data Base to Database when referring to the CSD + Fixed four occurrances of 'the the' in definitions + Added _item_range.maximum and _item_range.minimum DDL items to _refine.ls_abs_structure_Flack and removed discussion of limits from the definition. + Changed two occurances of 'will be' to 'are' in the definition of _entity.type. + Changed ENTITY_NPOL to CHEM_COMP in definition of _entity.type. + Changes ATOM to HETATM for APS coordinates in Example 1 for the ATOM_SITE category + Corrected _item.category_id for _struct_mon_details.prot_cis. + Corrected _item.category_id for _refine_hist.details. + Rewrote header comments to emphasize use of the mmCIF listserver as the forum for the dictionary review process. ; 0.7.26 1995-09-25 ; Changes (PMDF): + Put single quotes around 5HVP in those examples where they were missing. + Fixed registration of '5VHP' in examples. + Fixed typos in definition of _diffrn_measurement.device_specific. + Added _item.name loop and parent-child tree to _chem_comp.type + Fixed _item.name for _phasing_mir_der.der_set_id + Fixed _item.name for _phasing_mir_der.native_set_id + Added _phasing_mir_der_refln.set_id to _item.name loops and parent-child tree of _phasing_set.id + Fixed two misspellings of reference (refence). ; 0.7.27 1995-09-27 ; Changes (JDW & SH): + Added _item_aliases.dictionary and _item_aliases.version to all alias items. + Added several missing aliases from cifdic.C94. + Added a few missing data type codes in chem_link_* + Modified all _item_range items to reflect the correction in DDL 2.1.1. Checked all of the boundary conditions on ranges. + Made corrections in virtually all of the regular expressions. + Added data types 'ucode' and 'uchar'. These are case insensitive character types for words and single line strings, respectively. The regular expressions for these items will match characters of upper and lower case but the primitive type is uchar so all comparisons are performed in upper case. This avoids problems with case, where case is really not important. + Reviewed all items with character data types and made the following changes (hopefully uniformly): - Data items with single word enumerates were set to type 'ucode'. - Data items with multi word enumerates were set to type 'uchar'. - Any item which could potentially exceed 80 characters was set to type text. - Items which are restricted to single words were set to type 'code'. - Items which are short strings which may not span lines were set to type 'char'. + Moved aliases for anisotropic temperature factors from category ATOM_SITE to ATOM_SITE_ANISOTROP + Added category DATABASE_PDB_MATRIX to hold the SCALE and ORIGX matrices/vectors. + Modified the defintions of data types 'char1' and 'char3' to permit leading '+' to indicate a modification. + Checked dictionary with SIFLIB and returned to Paula ... ; 0.7.28 1995-10-06 ; Changes (PMDF): + Removed loop from category example for DATABASE_2 + Fixed data names in category example for STRUCT_KEYWORDS + Rewrote enumeration list for _struct_conf_type.id + Removed references to chemical_formula.appendix and replaced them with reference to the CHEMICAL_FORMULA category description + Added data items _chem_comp.formula and _chem_comp.formula_weight + Changed _chem_link_angle.atom_1_atom_id to _chem_link_angle.atom_id_1 + Changed _chem_link_angle.atom_2_atom_id to _chem_link_angle.atom_id_2 + Changed _chem_link_angle.atom_3_atom_id to _chem_link_angle.atom_id_3 + Changed _chem_link_bond.atom_1_atom_id to _chem_link_bond.atom_id_1 + Changed _chem_link_bond.atom_2_atom_id to _chem_link_bond.atom_id_2 + Realphabetized to accomodation the above changes + Added CHEM_LINK_CHIR category + Added CHEM_LINK_CHIR_ATOM category + Added CHEM_LINK_PLANE category + Added CHEM_LINK_PLANE_ATOM category + Added CHEM_LINK_TOR category + Added CHEM_LINK_TOR_VALUE category + Added entries to parent/child table for _chem_link.id for reflect the addition of the new categories. + Added Engh and Huber/Priestle examples to CHEM_LINK_BOND and CHEM_LINK_ANGLE + Realphabetized categories in PHASING_MAD section Changes (JDW): + Added _item_type.code's for _chem_link_chir*.atom_id and _chem_link_tor.atom_id_*. ; 0.7.29 1995-12-11 ; Changes (PMDF): + Changes to my title and Brian's in header information. + Enhanced description of the 'Hill system' of element ordering in the definition of _chem_comp.formula. + Added _item.mandatory_code to _phasing_mir_der.native_set_id + Added DATABASE_PDB_CAVEAT category. + Changed supercedes to superseded in DATABASE category description. + Changed DATABASE_NEW to DATABASE_2 in category description. + Changed SRUCT_SHEET_TOPOLOGY to STRUCT_SHEET_TOPOLOGY in category description. + Changed examples for STRUCT_SHEET_RANGE to contain only _struct_sheet_range.symmetry, not _struct_sheet_range.beg_symmetry and _struct_sheet_range.end_symmetry + Added cell.Z_PDB data item + Changed _atoms_sites.Cartn_tran_matrix to atom_sites.Cartn_transf_matrix in definition of _atom_sites.Cartn_transform_axes + Changed _chem_comp.nstd_class to _chem_comp.mon_nstd_class in definition of _chem_comp.mon_nstd_flag + Added data items for _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd + Changed reference to _chemical_formula.appendix to CHEMICAL_FORMULA category description in definition of _chemical_formula.moiety + Changed _comp.prog.version to _comp_prog.version and _comp.prog.citation_id to _comp_prog.citation_id in COMP_PROG example + Changed reference to _computing.phasing_mir in _phasing_mir.method to a reference to the COMP_PROG category. Similarly with _computing.phasing_averaging in _phasing_averaging.method and _computing.phasing_mad in _phasing_mad.method and _computing.save_reduction in _reflns.data_reduction_method + Changed _entity.name_com.name to _entity_name_com.name in ENTITY_NAME_COM example + Changed reference to _exptl_crystal.face_ to data items in the EXPTL_CRYSTAL_FACE category in the definition of _exptl_crystal.description. + Changed _diffrn.attenuator_code to _diffrn_attenuator.code in the definition of _diffrn_refln.attenuator_code + Changed _exptl.crystal_preparation to _exptl_crystal.preparation in the definition of _exptl.details + Changed _geom_bond.distance to _geom_bond.dist in the definition of _geom_bond.dist_esd + Added data items for _refine.ls_d_res_high and _refine.ls_d_res_low + Changed _refine.d_res_high to _refine.ls_d_res_high and _refine.d_res_low to _refine.ls_d_res_low in the definition of _refln.status + Changed _reflns_scale_group.code to _reflns_scale.group_code in the definition of _refln.scale_group_code + Changed _struct_site_view_details to _struct_biol_view.details in the rotation matrix element definitions in the STRUCT_BIOL_VIEW category (even though I realize that this isn't really correct in terms of the definition of _struct_biol_view.details) + Changed _symmetry.equiv_pos_as_xyz to _symmetry_equiv.pos_as_xyz in the definition of _symmetry.space_group_name_H-M + Changed _struct_mon.details_RSSR to _struct_mon_details.RSSR and _struct_mon.details_RSR to _struct_mon_details.RSR in a number of definitions in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories + Changed _reflns_shell.possible_%_obs to _reflns_shell.percent_possible_obs in the REFLNS_SHELL example + Corrected alphabetical order of data items in the REFLNS_SHELL category + Changed _struct_sheet.number_details to _struct_sheet.details in the STRUCT_SHEET examples + Replaced _struct_sheet_range.beg_symmetry and _struct_sheet_range.end_symmetry with _struct_sheet_range.symmetry in the STRUCT_SHEET_RANGE category and fixed example itself + Changed _refine.ls_number_reflns to _refine.ls_number_reflns_obs in the definitions of _refine.ls_restrained_S_all and _refine.ls_restrained_S_obs + Changed _refine_ls_shell.reflns to _refine_ls_shell.number_reflns_obs in the REFINE_LS_SHELL example + Removed example from DATABASE category as it was not longer valid ; 0.7.30 1996-01-29 ; Changes (PMDF, HB, JDW): + Added data items for pseudorotation in STRUCT_MON_NUCL. + Globally changed future tense usage to present tense (eg. will be -> is) + Added _citation.book_publisher_city. + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD. + Added _citation.journal_coden_CAS. + Generalized the defintion of _atom_site.calc_flag. + Corrections to definitions defining beginning and ends of ranges in category STRUCT_SHEET_HBOND. + Added data items _diffrn_refln.scan_rate and _diffrn_refln.scan_time_backgd + Added HELX_LH_27_P and HELX_RH_27_P helix enumeration types. + Added figure of merit data item _refln.fom. ; 0.7.31 1996-02-12 ; Changes (JDW): + Added data items for _database_pdb_matrix.tvect_matrix[][] and _database_pdb_matrix.tvect_vector[]. + Generalized category CHEM_LINK to handle descriptions of a any type of linkage. Created CHEM_COMP_LINK to describe linkages between components, and ENTITY_LINK to describe linkages between entities (and within entities between nonsequential components). Both CHEM_COMP_LINK and ENTITY_LINK reference the linkage description in the CHEM_LINK_* categories. ; 0.7.32 1996-02-17 ; Changes (JDW): + atom_site.entity_id renamed atom_site.label_entity_id. + atom_site.entity_seq_num deleted. + added items _atom_site.auth_asym_id, _atom_site.auth_atom_id, _atom_site.auth_comp_id, and _atom_site.auth_seq_id. These items provide placeholders for alternative nomenclature that may be used by the author. + Set the parentage for _atom_site.label_seq_id to _entity_poly_seq.num. All components of the atom site label (_atom_site.label_*) are now linked to the mmCIF hierarchical description of structure. The data items in _atom_site.auth_* may be used by authors to provide alternative identifiers in the atom site which conform with the scheme that is used in the publication of the structure. + added category group mm_atom_site_auth_label + added auth_asym_id, auth_atom_id, auth_comp_id, and auth_seq_id child data items to the categories: GEOM_ANGLE,GEOM_BOND, GEOM_CONTACT, STRUCT_CONF, STRUCT_CONN, STRUCT_MON_NUCL, STRUCT_PROT, STRUCT_PROT_CIS, STRUCT_NCS_DOM_GEN, STRUCT_SHEET_HBOND, STRUCT_SHEET_RANGE, and STRUCT_SITE_GEN. ; 0.7.33 1996-02-19 ; Changes (JDW): + Replaced category COMP_PROG with category SOFTWARE supplied by P. Bourne. + Fine tuned some values of _item_type.code. Fixed regular expression for code and ucode. ; 0.7.34 1996-02-20 ; Changes (JDW): + Integrated STRUCT_REF, STRUCT_REF_SEQ and STRUCT_REF_SEQ_DIF from PMDF. + Removed ENTITY_REFERENCE and ENTITY_POLY_SEQ_DIF. + Integrated modified categories STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, and STRUCT_NCS_OPER from PMDF. + changed _item_type.code's 'char' and 'uchar' to 'line' and 'uline'. ; 0.8.0 1996-03-06 ; Changes (PMDF, HB, JDW): + Added unit type 8pi2_angstroms_squared B anisotropic temperature factors, and added conversion factor for this new unit type in the ITEM_UNITS_CONVERSION category. + Changed _item_type.code for _symmetry_equiv.id to 'code' + Added default value 'no' to _chem_comp.mon_nstd_flag. ; 0.8.01 1996-03-12 ; Changes (PMDF): + Added missing circumflex to definition of _exptl_crystal.density_percent_sol. + Fixed erroneous reference to _atom_site.entity_seq_num in definition of _atom_site.auth_seq_id. + Changed _chem_comp_link.id to _chem_link.id in definition of _chem_comp_link.link_id. + Changed _citation.journal_coden_PDB to _citation.journal_coden_CSD in citation category example + Changed _entity_link.id to _chem_link.id in definition of _entity_link.link_id. + Changed _chem_link.type_comp_1 to _chem_comp_link.type_comp_1 in _item_name and parent/child tables for _chem_comp.type. The same change was made for component 2. ; 0.8.02 1996-03-18 ; Changes (PMDF): + Changed category from chem_comp to chem_comp_link for data items _chem_comp_link.type_comp_1 and _chem_comp_link.type_comp_1 in the parent/child tree for the chem_comp.type data item. + Added _struct_ref_seq.seq_align_beg and _struct_ref_seq.seq_aling_end to the mandatory code table for _entity_poly_seq.num. + Added _struct_ref_seq_dif.seq_num to both the parent/child and mandatory code tables for _entity_poly_seq.num. + Added data item _struct_ncs_oper.code. + Changed units type to 8pi2_angstroms_squares for _atom_site.B_iso_or_equiv and _atom_site.B_iso_or_equiv_esd. + Moved TVECT vector from DATABASE_PDB_MATRIX to a new category DATABASE_PDB_TVECT and added a identifier and details item to this new category. The matrix component of TVECT has been removed. ; 0.8.03 1996-04-03 ; Changes (PMDF): + Began implementing changes to bring this dictionary into alignment with the current version of the CIF core dictionary. These differences were provided by Brian McMahon and I. David Brown. As most of these changes are matters of style and not substance, they will not be noted individually here. Anything that does involve substance will be. + Changed specification of the format of names to included that provision for a dynanastic modifier. ; 0.8.04 1996-11-04 ; Changes (PMDF): + Changed format of references in data item definitions to match style of extended core. + Changed format of matrices in data item definitions to match style of extended core, with the addition of more rigorous definition of style agreed to by PMDF, JDW and HB. + Changed format of equivations in data item definitions to match style of extended core, with the addition of more rigorous definition of style agreed to by PMDF, JDW and HB. + Added aliases to data items where they were missing to establish correspondence with extended core. + Changed frac to fract in _atom_site.frac... data items. + Added _citation_editor_ordinal. + Added JOURNAL_INDEX data items, as well as _journal.language and _journal.paper_category. + Added _diffrn_measurement_specimen_support _diffrn_orient_refln_angle_omega _diffrn_orient_refln_angle_theta + Added PUBL_BODY category and data items. + Added _publ.contact_author_address _publ.contact_author_name + Added _publ.section_exptl_solution _publ.section_synopsis _publ.section_title_footnote + Added AUDIT_CONFORM category and data items. + Added GEOM_HBOND category and data items. ; 0.8.05 1996-11-11 ; Changes (PMDF): + More changes to bring this dictionary into alignement with the extended core + Added _chemical_forumula.iupac + Added _atom_site.B_equiv_geom_mean (and its esd) + Added _atom_site.U_equiv_geom_mean (and its esd) + Added _atom_type.scat_length_neutron ; 0.8.06 1996-11-13 ; Changes (JDW): + Reorganized categories in the DIFFRN group to formally support multiple diffraction data sets. ; 0.8.07 1996-12-18 ; Changes (PMDF): + Removed single quote from value of DDL items where they were not needed + Cleaned up style of range minimum/maximum data value + Cleaned up alignment of various DDL items + Deleted _chem_link_bond.value_angle and _chem_link_bond.value_angle_esd ; 0.8.08 1997-01-06 ; Changes (PMDF): + Added R_work data items to the various REFINE categories + Rewrote definitions for existing R-factor definitions to distinguish between R_work, R_free and conventional R Changes (JDW) (retrieved from earlier, misplaced version): + Added data item _chem_comp.mon_nstd_parent_comp_id to provide explicit reference between a nonstandard component and the parent component. + Changed _item_type.code for _chem_comp.id and all of its children to 'ucode'. + Changed char3 and char1 to uchar3 and uchar1 to be consistent with other case insensitive data type codes. Corrected the regular expressions and primitive codes for these data types. + Added _chem_comp_atom.partial_charge. + Corrected the descriptions for _chem_comp_tor.comp_id, _chem_comp_bond.comp_id and _chem_comp_angle.comp_id. + Added _chem_comp_tor_value.comp_id as a key for category CHEM_COMP_TOR_VALUE. + Added _chem_comp_plane_atom.comp_id as a key in category CHEM_COMP_PLANE_ATOM. + Miscellaneous corrections in item descriptions in CHEM_COMP_GROUP categories. + Added item _chem_comp_plane_atom.dist_esd ; 0.8.09 1997-01-07 ; Changes (PMDF): + More changes to align with new core: Changed _citation.book_coden_ISBN to _citation.book_id_ISBN Changed _citation.journal_coden_ASTM to _citation.journal_id_ASTM Changed _citation.journal_coden_CAS to _citation.abstract_id_ASTM Changed _citation.journal_coden_CSD to _citation.journal_id_CSD Changed _citation.journal_coden_ISSN to _citation.journal_id_ISSN Changed _citation.medline_AN to _citation.database_id_Medline Added _publ.requested_category Corrected alias for _atom_type.scat_length_neutron Added _journal.data_validation_number Changed _diffrn_detector.detector_specific to _diffrn_detector.type Deleted _diffrn_detector.detector_type Added _diffrn_radiation.probe Adjusted definition of _diffrn_radiation.type Changed _diffrn_source.source_specific to _diffrn_source.type Deleted old _diffrn_source.type Changed _diffrn_radiation_wavelength.wavelength_wt to _diffrn_radiation_wavelength.wt Added _diffrn_radiation.xray_symbol Aliased both versions 1.0 and 2.0 of the core for _diffrn_detector.detector _diffrn_detector.dtime _diffrn_source.source ; 0.8.10 1997-01-22 ; Changes (PMDF): + Still more changes to align with new core: Added _refine.ls_R_Fsqd_factor_obs Added _refine.ls_R_I_factor_obs Added _atom_site.disorder_assembly Added new definition of _atom_site.disorder_group Many more style and wording changes Changes to provide compatibility with PDB Remark 3 Added _chem_comp_chir_atom.comp_id Added _diffrn.ambient_temp_details Added _exptl_crystal_grow.temp_details Enlarged enumeration list of _phasing.method Added _reflns.Rmerge_F_all Added _reflns.Rmerge_F_obs Added _reflns.B_iso_Wilson_estimate Added _reflns.percent_possible_obs Added _refine_ls_restr.weight Added _refine.aniso_B data items Added _exptl_crystal.density_matthews Added _refine.ls_percent_reflns_R_free Added _refine_ls_shell.percent_reflns_R_free Added _refine.Luzzati_coordinate_error_obs Added _refine.Luzzati_d_res_low_obs Added _refine.Luzzati_sigma_a_obs Added _refine.Luzzati_sigma_a_obs_details Added _refine.Luzzati_coordinate_error_free Added _refine.Luzzati_d_res_low_free Added _refine.Luzzati_sigma_a_free Added _refine.Luzzati_sigma_a_free_details Added _refine.number_disordered_residues Added _refine.occupancy_sum_hydrogen Added _refine.occupancy_sum_non_hydrogen ; 0.8.11 1997-01-22 ; Changes (PMDF): Enforced style of only one space at the end of a sentence and after a ; Enforced stye in the categories section Enforced style of Need example 1 + More changes to provide compatibility for PDB Remark 3 Added _refine.B_iso_mean Added _refine.ls_percent_reflns_obs Added _refine.ls_R_factor_R_free_error Added _refine.ls_R_factor_R_free_error_details Added _refine_ls_shell.percent_reflns_obs Added _refine_ls_shell.R_factor_R_free_error Added _refine_ls_shell.redundancy_reflns_all Added _refine_ls_shell.redundancy_reflns_obs Added _refine.ls_redundancy_reflns_all Added _refine.ls_redundancy_reflns_obs Added _reflns.observed_criterion_sigma_F Added _reflns.observed_criterion_sigma_I Added REFINE_LS_RESTR_NCS category Added _refine.solvent_model_details Added _refine.solvent_model_param_bsol Added _refine.solvent_model_param_ksol ; 0.8.12 1997-01-28 ; Changes (JDW): Replaced all tabs with spaces. Fixed instances of lines > 80 characters. Added 'GLX' to the enumeration list for _chem_comp.three_letter_code. Added 'B' and 'Z' to the enumeration list for _chem_comp.one_letter_code. Corrected definition for _cell_measurement.wavelength. Corrected definitions for _atom_type.scat_dispersion_imag and _atom_type.scat_dispersion_real. Corrected examples for categories: CITATION, DIFFRN_DETECTOR, DIFFRN_MEASUREMENT, DIFFRN_SOURCE, GEOM_HBOND, REFINE_ANALYZE, REFINE_LS_RESTR, Corrected definition for _reflns_shell.Rmerge_F_obs. Corrected definition for _reflns_scale.group_code. Changed _refine_ls_restr_ncs.weight_iso_B to _refine_ls_restr_ncs.weight_B_iso. Corrected definitions in: _diffrn_refln.angle_[chi-theta]. Using experimental data kindly provided by Tom Emge, Shri Jain, Rachel Kramer, Jinsong Liu, and Gary Parkinson examples were added for the following categories: DIFFRN_ORIENT_MATRIX, DIFFRN_ORIENT_REFLN, DIFFRN_REFLN, DIFFRN_SCALE_GROUP, EXPTL, EXPTL_CRYSTAL, EXPTL_CRYSTAL_FACE, STRUCT_REF_SEQ, STRUCT_REF_SEQ_DIF, STRUCT_NCS_OPER, STRUCT_NCS_DOM, STRUCT_NCS_DOM_LIM, STRUCT_NCS_ENS, STRUCT_NCS_ENS_GEN, REFINE_LS_RESTR_NCS, PHASING_MIR_DER_REFLN, PHASING_SET, PHASING_SET_REFLN, STRUCT_MON_NUCL, STRUCT_MON_PROT, REFINE_HIST, ATOM_SITE_ANISOTROP, CHEM_COMP_LINK, JOURNAL, PUBL, CELL_MEASUREMENT_REFLN, CHEMICAL, CHEMICAL_CONN_ATOM, CHEMICAL_CONN_BOND, STRUCT_BIOL_VIEW, STRUCT_SITE_VIEW, STRUCT_MON_PROT_CIS. Added _exptl_crystal_face.crystal_id. Added items: _reflns.observed_criterion_I_min _reflns.observed_criterion_I_max _reflns.observed_criterion_F_max _reflns.observed_criterion_F_min. Changed dictionary tile and data block name to the conforming name recommended by SRH/BMcM, cif_mm.dic. Restore consistency to the 'arbitrary units' suffix: Changed _phasing_set_refln.F_meas_au_sigma to _phasing_set_refln.F_meas_sigma_au Changed _phasing_mir_der_refln.F_meas_au_sigma to _phasing_mir_der_refln.F_meas_sigma_au Changed _phasing_set_refln.F_meas_au_sigma to _phasing_set_refln.F_meas_sigma_au Changed _refln.F_meas_au_sigma to _refln.F_meas_sigma_au Although data item names and category names are not case sensitive, as a matter of style certain abbreviations are consistently expressed in upper case (e.g. B, MIR, MAD, PDB). Corrected definition for category DATABASE. Added category ENTRY_LINK and corresponding aliases to CIF core category audit_link. Corrected alias name _refine_ls_R_I_factor. Added core CIF alias _diffrn_refln_crystal_id to data item _diffrn.crystal_id. ; 0.9.0 1997-01-30 ; Changes (PMDF): + Corrected _reflns_observed_criterion to _reflns.observed_criterion in a number of places + Aligned enumeration lists in this dictionary with those in version 2.0 of the core dictionary. This involved changes in: _citation.coordinate_linkage _diffrn_radiation.xray_symbol _diffrn_refln.scan_mode _diffrn_refln.scan_mode_backgd _exptl.absorpt_correction_type _publ_manuscript_incl.extra_defn _refine.ls_hydrogen_treatment _refine.ls_structure_factor_coef + A number of corrections to errors pointed out by H. Bernstein Added category.id to _database_PDB_tvect.id Fixed spelling of _publ.section_exptl_soltuion Corrected _refine.ls_R_factor_work to _refine.ls_R_factor_R_work in description Corrected spelling of _refine_analyze.Luzaatti_d_res_low_obs in example Corrected spelling of _refine_analyze.Luzzatti_coordinate_error_obs in example Corrected _geom_hbond.atom_site_label_id_D to _geom_hbond.atom_site_id_D in example Corrected _geom_hbond.atom_site_label_id_H to _geom_hbond.atom_site_id_H in example Corrected _geom_hbond.atom_site_label_id_A to _geom_hbond.atom_site_id_A in example Corrected _entry_link.description to _entry_link.details Corrected _DIFFRN_SCALE_GROUP to DIFFRN_SCALE_GROUP in description Corrected _refine_ls_restr_ncs.model_details to _refine_ls_restr_ncs.ncs_model_details in example Corrected _refln.observed_criterion to _reflns.observed_criterion in description Corrected _struct_biol_view.view_id to _struct_biol_view.id in example Corrected _chem_comp_link.id to _chem_comp_link.link_id in example Corrected _chem_comp_link.comp_type_1 to _chem_comp_link.type_comp_1 Corrected _chem_comp_link.comp_type_1 to _chem_comp_link.type_comp_1 Corrected _entry_link.link_id to _entry_link.entry_id in description Changes (JDW): Corrections to REFINE_HIST category example and removal of a few misplaced colons. ; 0.9.01 1997-01-31 ; Changes (PMDF): + Removed occurrance of two or more blank lines + Enforced rule of no apostrophes around values for _item_sub_category.id + Enforced rule of no apostrophes around values for_item_default.value + Enforced rule of no apostrophes around values for_item.mandatory_code and fixed one alignment problem + Enforced rule of no apostrophes around values for _item_related.function_code and fixed a few alignment problems + Added _item.mandatory_code for _diffrn_refln.wavelength_id + Changed cifdic.c94 to cif_core.dic in _item_aliases.dictionary everywhere + Changed 2.0 to 2.0.1 in _item_aliases.version everywhere + Changed to consistent usage of kelvins instead of kelvin, got rid of capitalized versions + Removed capitalized usages of angstroms + Enforced rule of no apostrophes around values for _item_units.code + Fixed alignment problems with a few _category_key.name values ; 1.0.00 1997-10-14 ; Changes (PMDF): + Editorial changes in light of proof-reading by B. McMahon and I.D. Brown + No data names or enumeration values have changed, with the exception of the addition of the enumeration value 'other' to exptl.method + The bulk of the changes, which are too numerous to list there, were fixing spelling and grammar errors, and providing missing definitions + In a few cases, data definitions were reworded for clarity + Replaced erroneous occurances of Y~calc~ with Y~obs~ in the defintions of weighted R factors (Ian Tickle) ; 2.0.01 2000-10-17 ; Changes (JDW): + Integrated new definitions and extensions to existing categories. Additional data definitions submitted by Kim Henrick. Content of phasing definitions reviewed by Paula Fitgerald. Content of refinement definitions reviewed by Dale Tronrud. Editorial review by Helen Berman, John Westbrook, and Paula Fitzgerald. New Items included in this version: _phasing_MIR.d_res_high, _phasing_MIR.d_res_low, _phasing_MIR.FOM, _phasing_MIR.FOM_acentric, _phasing_MIR.FOM_centric, _phasing_MIR.reflns, _phasing_MIR.reflns_acentric, _phasing_MIR.reflns_centric, _phasing_MIR.reflns_criterion, _phasing_MIR_der.power_acentric, _phasing_MIR_der.power_centric, _phasing_MIR_der.R_cullis_acentric, _phasing_MIR_der.R_cullis_anomalous, _phasing_MIR_der.R_cullis_centric, _phasing_MIR_der.reflns_acentric, _phasing_MIR_der.reflns_anomalous, _phasing_MIR_der.reflns_centric, _phasing_MIR_der_site.occupancy_anom, _phasing_MIR_der_site.occupancy_anom_su, _phasing_MIR_der_site.occupancy_iso, _phasing_MIR_der_site.occupancy_iso_su, _phasing_MIR_shell.FOM_acentric, _phasing_MIR_shell.FOM_centric, _phasing_MIR_shell.reflns_acentric, _phasing_MIR_shell.reflns_anomalous, _phasing_MIR_shell.reflns_centric, _refine.correlation_coeff_Fo_to_Fc, _refine.correlation_coeff_Fo_to_Fc_free, _refine.overall_SU_B, _refine.overall_SU_ML, _refine.overall_SU_R_Cruickshank_DPI, _refine.overall_SU_R_free, _refine.overall_FOM_free_R_set, _refine.overall_FOM_work_R_set, _refine_analyze.RG_d_res_high, _refine_analyze.RG_d_res_low, _refine_analyze.RG_free, _refine_analyze.RG_work, and _refine_analyze.RG_free_work_ratio. + New categories included in this version: REFINE_FUNCT_MINIMIZED,REFINE_LS_RESTR_TYPE, REFLN_SYS_ABS. + Modification of examples for _refine_ls_restr.type + Contributed editorial and typographical corrections. + Corrected incomplete keys in categories PHASING_MAD_SET and DATABASE_PDB_REV_RECORD. + _exptl.method enumerations moved to examples. + Added database codes for RCSB and EBI. + Fixed item examples in _publ_body.label. ; 2.0.02 2000-10-24 ; Changes (JDW): + Updated enumerations for _database_PDB_rev.mod_type. + Updated enumerations for _struct_conn_type.id + Corrected data type of _refine_ls_shell.percent_reflns_obs from int to float + Updated preliminary description of _database_PDB_rev.status. + Changed regular expression for float to accept trailing decimal (ie. dd.) + Add () to regular expressions for code and ucode. + Added L-saccharide, D-saccharide, saccharide to enumerants for _chem_comp.type to handle monosaccarided components where linking cannot be inferred. ; 2.0.03 2000-11-09 ; Changes (JDW): + Relax regular expression for atom names to accept blanks in atom names in order to support nomenclature used in many existing macromolecular data files. Data type "atcode" has been assigned to _chem_comp_atom.atom_id, _atom_site.auth_atom_id and all related items. ; 2.0.04 2004-04-21 ; Changes (JDW): + Changed working name and packaging of dictionary. + _reflns_shell_number_possible range data type error fixed + Fix syntax errors in category examples. + Remove nonsense zero value default values + Remove all default values from *_esd items + Make _atom_site.label_* mandatory + Make _atom_site.auth_asym_id mandatory + Make _software.citation_id optional ; 2.0.05 2004-08-04 ; Changes (JDW): + Changed data type of _refine.ls_redundancy_reflns_all, _refine.ls_redundancy_reflns_obs, _refine_ls_shell.redundancy_reflns_all, _refine_ls_shell.redundancy_reflns_obs from int to float. ; 2.0.06 2005-03-03 ; Changes (JDW): + The following data items added to maintain data item correspondence with the CIF CORE dictionary V 2.3. All aliases in section 1 updated to version 2.3. _atom_site.adp_type _atom_site.refinement_flags _atom_site.refinement_flags_adp _atom_site.refinement_flags_occupancy _atom_site.refinement_flags_posn _atom_sites.special_details _atom_type.scat_dispersion_source _audit_link.block_code _audit_link.block_description _cell.reciprocal_angle_alpha _cell.reciprocal_angle_beta _cell.reciprocal_angle_gamma _cell.reciprocal_angle_alpha_esd _cell.reciprocal_angle_beta_esd _cell.reciprocal_angle_gamma_esd _cell.reciprocal_length_a _cell.reciprocal_length_b _cell.reciprocal_length_c _cell.reciprocal_length_a_esd _cell.reciprocal_length_b_esd _cell.reciprocal_length_c_esd _cell.special_details _chemical.absolute_configuration _chemical.melting_point_gt _chemical.melting_point_lt _chemical.optical_rotation _chemical.properties_biological _chemical.properties_physical _chemical.temperature_decomposition _chemical.temperature_decomposition_esd _chemical.temperature_decomposition_gt _chemical.temperature_decomposition_lt _chemical.temperature_sublimation _chemical.temperature_sublimation_esd _chemical.temperature_sublimation_gt _chemical.temperature_sublimation_lt _citation.database_id_CSD _database.CSD_history _database.code_CAS _database.code_CSD _database.code_ICSD _database.code_MDF _database.code_NBS _database.code_PDB _database.code_PDF _database.code_depnum_ccdc_fiz _database.code_depnum_ccdc_journal _database.code_depnum_ccdc_archive _diffrn.ambient_pressure _diffrn.ambient_pressure_esd _diffrn.ambient_pressure_gt _diffrn.ambient_pressure_lt _diffrn.ambient_temperature _diffrn.ambient_temperature_esd _diffrn.ambient_temperature_gt _diffrn.ambient_temperature_lt _diffrn_attenuator.material _diffrn_detector.area_resol_mean _diffrn_detector.dtime _diffrn_refln.class_code _diffrn_refln.intensity_u _diffrn_reflns.av_unetI/netI _diffrn_reflns_class.av_R_eq _diffrn_reflns_class.av_sgI/I _diffrn_reflns_class.av_uI/I _diffrn_reflns_class.code _diffrn_reflns_class.description _diffrn_reflns_class.d_res_high _diffrn_reflns_class.d_res_low _diffrn_reflns_class.number _diffrn_source.take-off_angle _diffrn_standards.scale_u _exptl_crystal.colour_lustre _exptl_crystal.colour_modifier _exptl_crystal.colour_primary _exptl_crystal.density_meas _exptl_crystal.density_meas_esd _exptl_crystal.density_meas_gt _exptl_crystal.density_meas_lt _exptl_crystal.density_meas_temp _exptl_crystal.density_meas_temp_esd _exptl_crystal.density_meas_temp_gt _exptl_crystal.density_meas_temp_lt _geom_bond.valence _publ_author.id_iucr _refine.ls_R_factor_gt _refine.ls_goodness_of_fit_gt _refine.ls_goodness_of_fit_ref _refine.ls_shift/esd_max _refine.ls_shift/esd_mean _refine.ls_shift/su_max _refine.ls_shift/su_max_lt _refine.ls_shift/su_mean _refine.ls_shift/su_mean_lt _refine_ls_class.code _refine_ls_class.d_res_high _refine_ls_class.d_res_low _refine_ls_class.R_factor_gt _refine_ls_class.R_factor_all _refine_ls_class.R_Fsqd_factor _refine_ls_class.R_I_factor _refine_ls_class.wR_factor_all _refln.class_code _refln.d_spacing _refln.include_status _refln.mean_path_length_tbar _refln.observed_status _refln.sint/lambda _reflns.Friedel_coverage _reflns.number_gt _reflns_class.code _reflns_class.description _reflns_class.d_res_high _reflns_class.d_res_low _reflns_class.number_gt _reflns_class.number_total _reflns_class.R_factor_all _reflns_class.R_factor_gt _reflns_class.R_Fsqd_factor _reflns_class.R_I_factor _reflns_class.wR_factor_all _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _space_group.crystal_system _space_group.id _space_group.IT_number _space_group.name_Hall _space_group.name_H-M_alt _space_group_symop.id _space_group_symop.operation_xyz _space_group_symop.sg_id _valence_param.atom_1 _valence_param.atom_1_valence _valence_param.atom_2 _valence_param.atom_2_valence _valence_param.B _valence_param.details _valence_param.id _valence_param.ref_id _valence_param.Ro _valence_ref.id _valence_ref.reference Changes (BM): 2005-03-03 Editorial changes to accompany International Tables Volume G publication (B. McMahon): + Fixed broken example loop for _phasing_MAD_ratio.* + Expanded the definitions for _phasing_MIR_der_refln.HL_A_iso (and B, C and D terms) and provided literature reference + Abbreviation .FOM (for figure-of-merit) consistently rendered lowercase + Expanded the definitions for _refine.solvent_model_param_bsol (and *_ksol) and provided literature reference + Rearranged the order of entries in the REFINE_ANALYZE category to preserve strict alphabetisation + Removed _refine_ls_restr_type.U_sigma_weights from example in REFINE_LS_RESTR_TYPE category + Commented out the incorrect example for the CHEM_COMP_LINK category + For the example in the ENTITY_NAME_SYS category supplied the EC number and the systematic name "water"; also trimmed the irrelevant last line of the definition. + Changed the vague 'x,x-pyranoside' example of _entity_name_sys.name to 'hydroquinone-beta-D-pyranoside' and matched this with 'arbutin' for _entity_name_com.name + Removed the CAVEAT and REMARK terms (and PDB code trailers) from the contents pf the _database_PDB_caveat.* and *_remark.* examples in accordance with current PDB practice + Updated reference to Tickle et al. in _refine_analyze.RG_free_work_ratio + Fixed few minor typos + Cosmetic reflowing of textual examples to aid typesetting + Added Engh & Huber and Priestle references to example details + Changed upper enumeration limit of _atom_site_attached_hydrogens to 8 in line with current Core dictionary + Added URL of PDB format description to _database_PDB_rev.mod_type + Extended enumeration list of _publ.requested_category for Acta E papers + Updated definition of _refine.ls_abs_structure_Flack and *_Rogers to reflect the more correct wording of the current Core dictionary. + Added _item_range.maximum and *minimum to _refine.ls_abs_structure_Rogers in line with new wording of definition. Changes (NJA): 2005-03-03 + Commented out duplicate save frames for following items with _item_aliases.version 2.0.1: _atom_site.refinement flags, _database.code_CAS, _database.code_CSD _database.code_ICSD, _database.code_MDF, _database.code_NBS _database.code_PDF, _diffrn.ambient_pressure, _diffrn.ambient_pressure.esd _diffrn_detector.dtime, _exptl_crystal.density.meas _exptl_crystal.density_meas_temp, _refln.mean_path_length_tbar Changes (BM): 2005-03-03 + Fixed erroneous _item.name in save__diffrn.ambient_pressure_esd + Removed erroneous aliases to *_esd quantities in coreCIF 2.3: _cell_reciprocal_angle_alpha_esd, _cell_reciprocal_angle_beta_esd _cell_reciprocal_angle_gamma_esd, _cell_reciprocal_length_a_esd _cell_reciprocal_length_b_esd, _cell_reciprocal_length_c_esd _chemical_temperature_decomposition_esd _chemical_temperature_sublimation_esd _diffrn.ambient_pressure_esd, _diffrn_ambient_temperature_esd _exptl_crystal_density_meas_esd, _exptl_crystal_density_meas_temp_esd + Removed redundant aliases: _cell.special_details ( = _cell.details) _diffrn.ambient_temperature ( = _diffrn.ambient_temp) _refine.ls_shift/esd_max ( = _refine.ls_shift_over_esd_max) _refine.ls_shift/esd_mean ( = _refine.ls_shift_over_esd_mean) _refln.observed_status ( = _refln.status) _refln.sint/lambda ( = _refln.sint_over_lambda) + Changed _refine.ls_shift/su_max to _refine.ls_shift_over_su_max and likewise for *_lt, *_mean and *_max_lt Changes (NJA): 2005-03-07 + Changed _reflns.class_d_res_low to _reflns_class.d_res_low in description of _reflns_class.wR_factor_all + Added [][] to _atom_sites.Cartn_transf_matrix, _diffrn_reflns.transf_matrix and _diffrn_orient_matrix.UB for consistency throughout. + Changed _chem_comp_link.type_1 and _2 to _chem_comp_link.type_comp_1 and 2 in _chem_link_angle.atom_id_1 and _2 + Changed all occurences of _diffrn.ambient_temperature to _diffrn.ambient_temp + Changed _diffrn_reflns.class_code to _diffrn_reflns_class.code in _diffrn_refln.class_code + Changed _geom_bond.distance to _geom_bond.dist in description of _geom_bond.valence. + Changed _refln.observed_status to _refln.status in refln.include_status + Changed _reflns.special_details to _reflns.details in _reflns.number_gt and _reflns_class.number_gt + Created new entry for _reflns.threshold_expression, as no entry existed and many item descriptions referred to _reflns_threshold_expression (these were then changed to _reflns.threshold_expression). + Changed _struct_mon_prot.alt_id, _struct_mon_prot.asym_id, _struct_mon_prot.comp_id and _struct_mon_prot.seq_id to _struct_mon_prot.label_alt_id, _struct_mon_prot.label_asym_id, _struct_mon_prot.label_comp_id and _struct_mon_prot.label_seq_id in Example 1 of _struct_mon_prot. + Changed _struct_site_view.view_id to _struct_site_view.id in Example 1 of _struct_site_view. ; 2.0.07 2005-03-03 ; Changes (JDW) 2005-03-08 + Changed related references to _diffrn.ambient_temperature to _diffrn.ambient_temp + Changed related references to _refln.observed_status to _refln.status + Restore original case to FOM - although case is not an issue for mmCIF it is an issue for XML translations. ; 2.0.08 2005-04-06 ; Changes (JDW) 2005-04-06 + Added mandatory code _cell.reciprocal_angle_beta ; 2.0.09 2005-06-27 ; Internal dates used for housekeeping prior to release 2005-04-13 Changes (NJA) 2005-04-13 + Minor corrections to spelling and punctuation. + pdb_group definition: Brookhaven Protein Data Bank changed to Protein Data Bank. 2005-04-14 Changes (NJA) 2005-04-14 + Minor corrections to spelling and punctuation. + _atom_sites.solution_* descriptions edited so each appropriate to the particular data name. +_chem_comp.formula description edited to match that in core dictionary +_chem_comp.three_letter_code: several typing errors in amino-acid and base names corrected. +_chem_comp_atom.model_Cartn_z: 'The x component ...' changed to 'The z component...' +_chemical.melting_point_* descriptions edited so each appropriate to the particular data name. +_chemical.temperature_decomposition_* descriptions edited so each appropriate to the particular data name. +_chemical.temperature_sublimation_* descriptions edited so each appropriate to the particular data name. 2005-04-15 Changes (NJA) 2005-04-15 + Minor corrections to spelling and punctuation. +_citation.journal_id_CSD description, Brookhaven Protein Data Bank changed to Protein Data Bank. +_database.code_* entries edited so each is relevant to the particular data name +_database_PDB_matrix.scale[3][3]: description changed from 'The [1][1] element of the PDB SCALE matrix.' to 'The [3][3] element of the PDB SCALE matrix.' +_diffrn.ambient_pressure_gt and _lt, descriptions edited so each is relevant to the particular data name. +_diffrn.ambient_temp_gt and _lt, descriptions edited so each is relevant to the particular data name. +_diffrn_attenuator.scale description changed to match that in the core dictionary. +_diffrn_radiation_wavelength.id: _diffrn_radiation_wavelength in description changed to _diffrn_radiation_wavelength.wavelength +_diffrn_reflns_class.av_sgI/I description [sum|u(net I)|/sum|net I|] changed to [sum|sigma(net I)|/sum|net I|] +_diffrn_reflns_class.d_res_high and _low descriptions changed to match those in the core dictionary +diffrn_source Example 1 _diffrn_source.power '50 kw, 180 mA' changed to _diffrn_source.power 50 and _diffrn_source.current 180 +_exptl_crystal.density_Matthews year of reference corrected from 1960 to 1968 +_exptl_crystal.density_meas_gt and _lt descriptions edited so each is relevant to the particular data name. +_exptl_crystal.density_meas_temp_gt and _lt descriptions edited so each is relevant to the particular data name. +geom_contact and geom_bond Example 1 year for reference corrected from 1991 to 1992 +_phasing_MAD_ratio.d_res_high and low ; _phasing_MAD_set.d_res_high and _low; _phasing_MIR.d_res_high and low; _phasing_MIR_der.d_res_high and low; _phasing_MIR_der_shell.d_res_high and low; _phasing_MIR_shell.d_res_high and low and _refine.ls_d_res_high and low rephrased to correspond to similar terms in the core dictionary. +Spelling of Lattman corrected in references to Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. +Temperature factor replaced by displacement parameter throughout. +refine Example 2 _refine.ls_weighting_scheme 'calc w=1/(\s^2^(F)+0.0004F^2^)' split into _refine.ls_weighting_scheme and _refine.ls_weighting_details +_refine.ls_extinction_coef and _refine.ls_extinction_method reference to Becker and Coppens corrected to 129-147, 148-153 (is two articles). +_refine.ls_restrained_S_all and _obs: Y~calc~ = the observed coefficients changed toY~calc~ = the calculated coefficients 2005-04-18 Changes (NJA) 2005-04-18 + Minor corrections to spelling and punctuation. + temperature factor changed to displacement parameter throughout + _refine_ls_class.R_factor_all 'and for significantly intense reflections (see _reflns.threshold_expression) ' removed from description. + _refine_ls_class.R_factor_gt 'for all reflections' removed from description. + _refine_ls_class.d_res_high and _low, _refine_analyze.RG_d_res_high and _low, _refine_ls_shell.d_res_high and _low, _reflns.d_resolution_high and low, _reflns_class.d_res_high and _low, _reflns_shell.d_res_high and _low definitions edited to match related definitions in the core dictionary + _refln.intensity_calc _meas, _sigma edited to match corresponding entries in the core dictionary + _reflns.Friedel_coverage in description _reflns_number_total changed to _reflns.number_all. + _reflns_class.R_factor_all 'and for significantly intense reflections (see _reflns.threshold_expression)' removed from description. + _reflns_class.R_factor_gt 'all reflections, and for' removed from description + _reflns_class.number_total in description: _reflns_special_details changed to _reflns.details 2005-04-19 Changes (NJA) 2005-04-19 + Minor corrections to spelling and punctuation. + _valence_param.ref_id description: _valence_ref_id changed to _valence_ref.id + References to International Tables updated. 2005-04-22 Changes (NJA) 2005-04-22 + _cell.reciprocal_angle_alpha, beta and gamma: descriptions edited so each appropriate to the particular data name. + _cell.reciprocal_length_a, b and c: descriptions edited so each appropriate to the particular data name. + _struct_mon_nucl.chi1 and _chi2; descriptions edited from `... sugar-base torsion angle chi...' to '... sugar-base torsion angle chi1' and '... sugar-base torsion angle chi2' 2005-05-03 Changes (NJA) 2005-05-03 + several data items *_esd edited so that the description reads 'the standard uncertainly of *', not 'the standard uncertainty of *_esd' + several DDL1 datanames in descriptions changed to DDL2 datanames 2005-05-10 Changes (NJA) 2005-05-10 + _citation.journal_id_CSD example changed from 070 to 0070 + Mursudov and Dodson (1997) references corrected + References to Cruickshank DPI updated + References to Luzzati (1952) corrected 2005-06-23 Changes (NJA) 2005-06-23 _publ_author.email added. Corrections for IT G Chapter 4.5 included. 2005-06-25 (BM) ITEM_UNITS_LIST: cosmetic changes to definitions of some units ITEM_UNITS_CONVERSION: multipliers in electrons per cubed terms fixed 2005-06-27 (BM) Some minor editorial changes to ensure consistency with latest pdbx dictionary version. Only significant change: + in _citation.id the listing for _software.citation_id has _item.mandatory_code changed to "no" to match the value in save__software.citation_id and to match pdbx ; ## ### EOF mmcif_std-header.dic #### ########################################################################### # # File: mmcif_std-data.dic # # mmCIF Data Dictionary (standard defintions) # # This data dictionary contains the standard mmCIF data definitions. # # Data Section # # ########################################################################### ################## ## SUB_CATEGORY ## ################## loop_ _sub_category.id _sub_category.description 'cartesian_coordinate' ; The collection of x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. ; 'cartesian_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to a Cartesian (orthogonal angstrom) coordinate system. ; 'fractional_coordinate' ; The collection of x, y, and z components of a position specified with reference to unit cell directions. ; 'fractional_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with reference to unit cell directions. ; 'matrix' ; The collection of elements of a matrix. ; miller_index ; The collection of h, k, and l components of the Miller index of a reflection. ; 'cell_length' ; The collection of a, b, and c axis lengths of a unit cell. ; 'cell_length_esd' ; The collection of estimated standard deviations of the a, b, and c axis lengths of a unit cell. ; 'cell_angle' ; The collection of alpha, beta, and gamma angles of a unit cell. ; 'cell_angle_esd' ; The collection of estimated standard deviations of the alpha, beta, and gamma angles of a unit cell. ; 'mm_atom_site_auth_label' ; The collection of asym id, atom id, comp id and seq id components of an author's alternative specification for a macromolecular atom site. ; 'mm_atom_site_label' ; The collection of alt id, asym id, atom id, comp id and seq id components of the label for a macromolecular atom site. ; 'vector' ; The collection of elements of a vector. ; ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; Categories that belong to the macromolecular dictionary. ; 'atom_group' 'inclusive_group' ; Categories that describe the properties of atoms. ; 'audit_group' 'inclusive_group' ; Categories that describe dictionary maintenance and identification. ; 'cell_group' 'inclusive_group' ; Categories that describe the unit cell. ; 'chemical_group' 'inclusive_group' ; Categories that describe chemical properties and nomenclature. ; 'chem_comp_group' 'inclusive_group' ; Categories that describe components of chemical structure. ; 'chem_link_group' 'inclusive_group' ; Categories that describe links between components of chemical structure. ; 'citation_group' 'inclusive_group' ; Categories that provide bibliographic references. ; 'computing_group' 'inclusive_group' ; Categories that describe the computational details of the experiment. ; 'compliance_group' 'inclusive_group' ; Categories that are included in this dictionary specifically to comply with previous dictionaries. ; 'database_group' 'inclusive_group' ; Categories that hold references to entries in databases that contain related information. ; 'diffrn_group' 'inclusive_group' ; Categories that describe details of the diffraction experiment. ; 'entity_group' 'inclusive_group' ; Categories that describe chemical entities. ; 'entry_group' 'inclusive_group' ; Categories that pertain to the entire data block. ; 'exptl_group' 'inclusive_group' ; Categories that hold details of the experimental conditions. ; 'geom_group' 'inclusive_group' ; Categories that hold details of molecular and crystal geometry. ; 'iucr_group' 'inclusive_group' ; Categories that are used for manuscript submission and internal processing by the staff of the International Union of Crystallography. ; 'pdb_group' 'inclusive_group' ; Categories that pertain to the file-format or data-processing codes used by the Protein Data Bank. ; 'phasing_group' 'inclusive_group' ; Categories that describe phasing. ; 'refine_group' 'inclusive_group' ; Categories that describe refinement. ; 'refln_group' 'inclusive_group' ; Categories that describe the details of reflection measurements. ; 'struct_group' 'inclusive_group' ; Categories that contain details about the crystallographic structure. ; 'symmetry_group' 'inclusive_group' ; Categories that describe symmetry information. ; #################### ## ITEM_TYPE_LIST ## #################### # # # The regular expressions defined here are not compliant # with the POSIX 1003.2 standard as they include the # '\n' and '\t' special characters. These regular expressions # have been tested using version 0.12 of Richard Stallman's # GNU regular expression library in POSIX mode. # # # For some data items, a standard syntax is assumed. The syntax is # described for each data item in the dictionary, but is summarized here: # # Names: The family name(s) followed by a comma, precedes the first # name(s) or initial(s). # # Telephone numbers: # The international code is given in brackets and any extension # number is preceded by 'ext'. # # Dates: In the form yyyy-mm-dd. # ############################################################################## loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail code char '[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; ucode uchar '[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; line char '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items ... ; uline uchar '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items (case insensitive)... ; text char '[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; int numb '-?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; float numb '-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?' ; float item types are the subset of numbers that are the floating numbers. ; name uchar '_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+' ; name item types take the form... ; idname uchar '[_A-Za-z0-9]+' ; idname item types take the form... ; any char '.*' ; A catch all for items that may take any form... ; yyyy-mm-dd char '[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]' ; Standard format for CIF dates. ; uchar3 uchar '[+]?[A-Za-z0-9][A-Za-z0-9][A-Za-z0-9]' ; data item for 3 character codes ; uchar1 uchar '[+]?[A-Za-z0-9]' ; data item for 1 character codes ; symop char '([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])?' ; symop item types take the form n_klm, where n refers to the symmetry operation that is applied to the coordinates in the ATOM_SITE category identified by _atom_site_label. It must match a number given in _symmetry_equiv_pos_site_id. k, l, and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used. These translations (x,y,z) are related to (k,l,m) by k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; atcode char '[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; Character data type for atom names ... ; ##################### ## ITEM_UNITS_LIST ## ##################### loop_ _item_units_list.code _item_units_list.detail # 'centimetres' 'centimetres (metres * 10^( -2))' 'millimetres' 'millimetres (metres * 10^( -3))' 'nanometres' 'nanometres (metres * 10^( -9))' 'angstroms' 'angstroms (metres * 10^(-10))' 'picometres' 'picometres (metres * 10^(-12))' 'femtometres' 'femtometres (metres * 10^(-15))' # 'reciprocal_metres' 'reciprocal metres (metres^(-1))' 'reciprocal_centimetres' 'reciprocal centimetres ((metres * 10^( -2))^(-1))' 'reciprocal_millimetres' 'reciprocal millimetres ((metres * 10^( -3))^(-1))' 'reciprocal_nanometres' 'reciprocal nanometres ((metres * 10^( -9))^(-1))' 'reciprocal_angstroms' 'reciprocal angstroms ((metres * 10^(-10))^(-1))' 'reciprocal_picometres' 'reciprocal picometres ((metres * 10^(-12))^(-1))' # 'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2' 'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2' '8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2' 'picometres_squared' 'picometres squared (metres * 10^(-12))^2' # 'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3' 'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3' 'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3' # 'kilopascals' 'kilopascals' 'gigapascals' 'gigapascals' # 'hours' 'hours' 'minutes' 'minutes' 'seconds' 'seconds' 'microseconds' 'microseconds' # 'degrees' 'degrees (of arc)' # 'degrees_per_minute' 'degrees (of arc) per minute' # 'celsius' 'degrees (of temperature) Celsius' 'kelvins' 'degrees (of temperature) Kelvin' # 'electrons' 'electrons' # 'electrons_squared' 'electrons squared' # 'electrons_per_nanometres_cubed' ; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3)) ; 'electrons_per_angstroms_cubed' ; electrons per angstroms cubed (electrons/(metres * 10^(-10))^(-3)) ; 'electrons_per_picometres_cubed' ; electrons per picometres cubed (electrons/(metres * 10^(-12))^(-3)) ; 'kilowatts' 'kilowatts' 'milliamperes' 'milliamperes' 'kilovolts' 'kilovolts' # 'megagrams_per_cubic_metre' 'megagrams per cubic metre' 'pixels_per_millimetre' 'pixels per millimetre' # 'arbitrary' ; arbitrary system of units. ; # loop_ _item_units_conversion.from_code _item_units_conversion.to_code _item_units_conversion.operator _item_units_conversion.factor ### 'centimetres' 'millimetres' '*' 1.0E+01 'centimetres' 'nanometres' '*' 1.0E+07 'centimetres' 'angstroms' '*' 1.0E+08 'centimetres' 'picometres' '*' 1.0E+10 'centimetres' 'femtometres' '*' 1.0E+13 # 'millimetres' 'centimetres' '*' 1.0E-01 'millimetres' 'nanometres' '*' 1.0E+06 'millimetres' 'angstroms' '*' 1.0E+07 'millimetres' 'picometres' '*' 1.0E+09 'millimetres' 'femtometres' '*' 1.0E+12 # 'nanometres' 'centimetres' '*' 1.0E-07 'nanometres' 'millimetres' '*' 1.0E-06 'nanometres' 'angstroms' '*' 1.0E+01 'nanometres' 'picometres' '*' 1.0E+03 'nanometres' 'femtometres' '*' 1.0E+06 # 'angstroms' 'centimetres' '*' 1.0E-08 'angstroms' 'millimetres' '*' 1.0E-07 'angstroms' 'nanometres' '*' 1.0E-01 'angstroms' 'picometres' '*' 1.0E+02 'angstroms' 'femtometres' '*' 1.0E+05 # 'picometres' 'centimetres' '*' 1.0E-10 'picometres' 'millimetres' '*' 1.0E-09 'picometres' 'nanometres' '*' 1.0E-03 'picometres' 'angstroms' '*' 1.0E-02 'picometres' 'femtometres' '*' 1.0E+03 # 'femtometres' 'centimetres' '*' 1.0E-13 'femtometres' 'millimetres' '*' 1.0E-12 'femtometres' 'nanometres' '*' 1.0E-06 'femtometres' 'angstroms' '*' 1.0E-05 'femtometres' 'picometres' '*' 1.0E-03 ### 'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01 'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07 'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08 'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10 # 'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01 'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06 'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07 'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09 # 'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07 'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06 'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01 'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03 # 'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08 'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07 'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01 'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02 # 'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10 'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09 'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03 'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01 ### 'nanometres_squared' 'angstroms_squared' '*' 1.0E+02 'nanometres_squared' 'picometres_squared' '*' 1.0E+06 # 'angstroms_squared' 'nanometres_squared' '*' 1.0E-02 'angstroms_squared' 'picometres_squared' '*' 1.0E+04 'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568 # 'picometres_squared' 'nanometres_squared' '*' 1.0E-06 'picometres_squared' 'angstroms_squared' '*' 1.0E-04 ### 'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03 'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09 # 'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03 'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06 # 'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09 'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06 ### 'kilopascals' 'gigapascals' '*' 1.0E-06 'gigapascals' 'kilopascals' '*' 1.0E+06 ### 'hours' 'minutes' '*' 6.0E+01 'hours' 'seconds' '*' 3.6E+03 'hours' 'microseconds' '*' 3.6E+09 # 'minutes' 'hours' '/' 6.0E+01 'minutes' 'seconds' '*' 6.0E+01 'minutes' 'microseconds' '*' 6.0E+07 # 'seconds' 'hours' '/' 3.6E+03 'seconds' 'minutes' '/' 6.0E+01 'seconds' 'microseconds' '*' 1.0E+06 # 'microseconds' 'hours' '/' 3.6E+09 'microseconds' 'minutes' '/' 6.0E+07 'microseconds' 'seconds' '/' 1.0E+06 ### 'celsius' 'kelvins' '-' 273.0 'kelvins' 'celsius' '+' 273.0 ### 'electrons_per_nanometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E+03 'electrons_per_nanometres_cubed' 'electrons_per_picometres_cubed' '*' 1.0E+09 # 'electrons_per_angstroms_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E-03 'electrons_per_angstroms_cubed' 'electrons_per_picometres_cubed' '*' 1.0E+06 # 'electrons_per_picometres_cubed' 'electrons_per_nanometres_cubed' '*' 1.0E-09 'electrons_per_picometres_cubed' 'electrons_per_angstroms_cubed' '*' 1.0E-06 ### ### EOF mmcif_std-data.dic ########################################################################### # # File: mmcif_std-def-1.dic # # mmCIF Data Dictionary (standard defintions) # # This data dictionary contains the standard mmCIF data definitions. # # Defintion Section 1 # # ########################################################################### ############### ## ATOM_SITE ## ############### save_atom_site _category.description ; Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. ; _category.id atom_site _category.mandatory_code no _category_key.name '_atom_site.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_site.group_PDB _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.footnote_id _atom_site.auth_seq_id _atom_site.id ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 11 1 ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 11 2 ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 11 3 ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 11 4 ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 11 5 ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 11 6 ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 11 7 ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 12 8 ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 12 9 ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 12 10 ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 12 11 ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 12 12 ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 12 13 ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 12 14 ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 12 15 ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 12 16 ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 13 17 ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 13 18 ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 13 19 ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 13 20 ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 13 21 ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 13 22 ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 13 23 # - - - - data truncated for brevity - - - - HETATM C C1 APS C . 1 4.171 29.012 7.116 0.58 17.27 1 300 101 HETATM C C2 APS C . 1 4.949 27.758 6.793 0.58 16.95 1 300 102 HETATM O O3 APS C . 1 4.800 26.678 7.393 0.58 16.85 1 300 103 HETATM N N4 APS C . 1 5.930 27.841 5.869 0.58 16.43 1 300 104 # - - - - data truncated for brevity - - - - ; save_ save__atom_site.aniso_B[1][1] _item_description.description ; The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][1]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][1]_esd' associated_esd '_atom_site.aniso_U[1][1]' conversion_constant '_atom_site_anisotrop.U[1][1]' conversion_constant '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][1]. ; _item.name '_atom_site.aniso_B[1][1]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][1]' associated_value '_atom_site.aniso_U[1][1]_esd' conversion_constant '_atom_site_anisotrop.U[1][1]_esd' conversion_constant '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][2] _item_description.description ; The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][2]_esd' associated_esd '_atom_site.aniso_U[1][2]' conversion_constant '_atom_site_anisotrop.U[1][2]' conversion_constant '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][2]. ; _item.name '_atom_site.aniso_B[1][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][2]' associated_value '_atom_site.aniso_U[1][2]_esd' conversion_constant '_atom_site_anisotrop.U[1][2]_esd' conversion_constant '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][3] _item_description.description ; The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][3]_esd' associated_esd '_atom_site.aniso_U[1][3]' conversion_constant '_atom_site_anisotrop.U[1][3]' conversion_constant '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][3]. ; _item.name '_atom_site.aniso_B[1][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][3]' associated_value '_atom_site.aniso_U[1][3]_esd' conversion_constant '_atom_site_anisotrop.U[1][3]_esd' conversion_constant '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][2] _item_description.description ; The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[2][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][2]_esd' associated_esd '_atom_site.aniso_U[2][2]' conversion_constant '_atom_site_anisotrop.U[2][2]' conversion_constant '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[2][2]. ; _item.name '_atom_site.aniso_B[2][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][2]' associated_value '_atom_site.aniso_U[2][2]_esd' conversion_constant '_atom_site_anisotrop.U[2][2]_esd' conversion_constant '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][3] _item_description.description ; The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[2][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][3]_esd' associated_esd '_atom_site.aniso_U[2][3]' conversion_constant '_atom_site_anisotrop.U[2][3]' conversion_constant '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[2][3]. ; _item.name '_atom_site.aniso_B[2][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][3]' associated_value '_atom_site.aniso_U[2][3]_esd' conversion_constant '_atom_site_anisotrop.U[2][3]_esd' conversion_constant '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[3][3] _item_description.description ; The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[3][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[3][3]_esd' associated_esd '_atom_site.aniso_U[3][3]' conversion_constant '_atom_site_anisotrop.U[3][3]' conversion_constant '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[3][3]. ; _item.name '_atom_site.aniso_B[3][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[3][3]' associated_value '_atom_site.aniso_U[3][3]_esd' conversion_constant '_atom_site_anisotrop.U[3][3]_esd' conversion_constant '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_ratio _item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site.aniso_ratio' _item.category_id atom_site _item.mandatory_code no _item_related.related_name '_atom_site_anisotrop.ratio' _item_related.function_code alternate_exclusive loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__atom_site.aniso_U[1][1] _item_description.description ; The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][1]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][1]_esd' associated_esd '_atom_site.aniso_B[1][1]' conversion_constant '_atom_site_anisotrop.B[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][1]. ; _item.name '_atom_site.aniso_U[1][1]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][1]' associated_value '_atom_site.aniso_B[1][1]_esd' conversion_constant '_atom_site_anisotrop.B[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][2] _item_description.description ; The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][2]_esd' associated_esd '_atom_site.aniso_B[1][2]' conversion_constant '_atom_site_anisotrop.B[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][2]. ; _item.name '_atom_site.aniso_U[1][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][2]' associated_value '_atom_site.aniso_B[1][2]_esd' conversion_constant '_atom_site_anisotrop.B[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][3] _item_description.description ; The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][3]_esd' associated_esd '_atom_site.aniso_B[1][3]' conversion_constant '_atom_site_anisotrop.B[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][3]. ; _item.name '_atom_site.aniso_U[1][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][3]' associated_value '_atom_site.aniso_B[1][3]_esd' conversion_constant '_atom_site_anisotrop.B[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][2] _item_description.description ; The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[2][2]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][2]_esd' associated_esd '_atom_site.aniso_B[2][2]' conversion_constant '_atom_site_anisotrop.B[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[2][2]. ; _item.name '_atom_site.aniso_U[2][2]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][2]' associated_value '_atom_site.aniso_B[2][2]_esd' conversion_constant '_atom_site_anisotrop.B[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][3] _item_description.description ; The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[2][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][3]_esd' associated_esd '_atom_site.aniso_B[2][3]' conversion_constant '_atom_site_anisotrop.B[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[2][3]. ; _item.name '_atom_site.aniso_U[2][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][3]' associated_value '_atom_site.aniso_B[2][3]_esd' conversion_constant '_atom_site_anisotrop.B[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[3][3] _item_description.description ; The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[3][3]' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[3][3]_esd' associated_esd '_atom_site.aniso_B[3][3]' conversion_constant '_atom_site_anisotrop.B[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[3][3]. ; _item.name '_atom_site.aniso_U[3][3]_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[3][3]' associated_value '_atom_site.aniso_B[3][3]_esd' conversion_constant '_atom_site_anisotrop.B[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.attached_hydrogens _item_description.description ; The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given. ; _item.name '_atom_site.attached_hydrogens' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_attached_hydrogens' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 0 0 0 _item_type.code int loop_ _item_examples.case _item_examples.detail 2 'water oxygen' 1 'hydroxyl oxygen' 4 'ammonium nitrogen' save_ save__atom_site.auth_asym_id _item_description.description ; An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_asym_id' atom_site yes '_geom_angle.atom_site_auth_asym_id_1' geom_angle no '_geom_angle.atom_site_auth_asym_id_2' geom_angle no '_geom_angle.atom_site_auth_asym_id_3' geom_angle no '_geom_bond.atom_site_auth_asym_id_1' geom_bond no '_geom_bond.atom_site_auth_asym_id_2' geom_bond no '_geom_contact.atom_site_auth_asym_id_1' geom_contact no '_geom_contact.atom_site_auth_asym_id_2' geom_contact no '_geom_hbond.atom_site_auth_asym_id_A' geom_hbond no '_geom_hbond.atom_site_auth_asym_id_D' geom_hbond no '_geom_hbond.atom_site_auth_asym_id_H' geom_hbond no '_geom_torsion.atom_site_auth_asym_id_1' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_2' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_3' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_4' geom_torsion no '_struct_conf.beg_auth_asym_id' struct_conf no '_struct_conf.end_auth_asym_id' struct_conf no '_struct_conn.ptnr1_auth_asym_id' struct_conn no '_struct_conn.ptnr2_auth_asym_id' struct_conn no '_struct_mon_nucl.auth_asym_id' struct_mon_nucl no '_struct_mon_prot.auth_asym_id' struct_mon_prot no '_struct_mon_prot_cis.auth_asym_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_asym_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_asym_id' struct_ncs_dom_lim no '_struct_sheet_range.beg_auth_asym_id' struct_sheet_range no '_struct_sheet_range.end_auth_asym_id' struct_sheet_range no '_struct_site_gen.auth_asym_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_angle.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_angle.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id' '_geom_bond.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_bond.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_contact.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_contact.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_A' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_D' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_H' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_4' '_atom_site.auth_asym_id' '_struct_conf.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conf.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conn.ptnr1_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conn.ptnr2_auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_nucl.auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_prot.auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_prot_cis.auth_asym_id' '_atom_site.auth_asym_id' '_struct_ncs_dom_lim.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_ncs_dom_lim.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_sheet_range.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_sheet_range.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_site_gen.auth_asym_id' '_atom_site.auth_asym_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_atom_id _item_description.description ; An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_atom_id' atom_site no '_geom_angle.atom_site_auth_atom_id_1' geom_angle no '_geom_angle.atom_site_auth_atom_id_2' geom_angle no '_geom_angle.atom_site_auth_atom_id_3' geom_angle no '_geom_bond.atom_site_auth_atom_id_1' geom_bond no '_geom_bond.atom_site_auth_atom_id_2' geom_bond no '_geom_contact.atom_site_auth_atom_id_1' geom_contact no '_geom_contact.atom_site_auth_atom_id_2' geom_contact no '_geom_hbond.atom_site_auth_atom_id_A' geom_hbond no '_geom_hbond.atom_site_auth_atom_id_D' geom_hbond no '_geom_hbond.atom_site_auth_atom_id_H' geom_hbond no '_geom_torsion.atom_site_auth_atom_id_1' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_2' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_3' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_4' geom_torsion no '_struct_conn.ptnr1_auth_atom_id' struct_conn no '_struct_conn.ptnr2_auth_atom_id' struct_conn no '_struct_sheet_hbond.range_1_beg_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_1_end_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_beg_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_end_auth_atom_id' struct_sheet_hbond no '_struct_site_gen.auth_atom_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_angle.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_angle.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id' '_geom_bond.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_bond.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_contact.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_contact.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_A' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_D' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_H' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_4' '_atom_site.auth_atom_id' '_struct_conn.ptnr1_auth_atom_id' '_atom_site.auth_atom_id' '_struct_conn.ptnr2_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_1_beg_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_1_end_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_2_beg_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_2_end_auth_atom_id' '_atom_site.auth_atom_id' '_struct_site_gen.auth_atom_id' '_atom_site.auth_atom_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code atcode save_ save__atom_site.auth_comp_id _item_description.description ; An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_comp_id' atom_site no '_geom_angle.atom_site_auth_comp_id_1' geom_angle no '_geom_angle.atom_site_auth_comp_id_2' geom_angle no '_geom_angle.atom_site_auth_comp_id_3' geom_angle no '_geom_bond.atom_site_auth_comp_id_1' geom_bond no '_geom_bond.atom_site_auth_comp_id_2' geom_bond no '_geom_contact.atom_site_auth_comp_id_1' geom_contact no '_geom_contact.atom_site_auth_comp_id_2' geom_contact no '_geom_hbond.atom_site_auth_comp_id_A' geom_hbond no '_geom_hbond.atom_site_auth_comp_id_D' geom_hbond no '_geom_hbond.atom_site_auth_comp_id_H' geom_hbond no '_geom_torsion.atom_site_auth_comp_id_1' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_2' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_3' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_4' geom_torsion no '_struct_conf.beg_auth_comp_id' struct_conf no '_struct_conf.end_auth_comp_id' struct_conf no '_struct_conn.ptnr1_auth_comp_id' struct_conn no '_struct_conn.ptnr2_auth_comp_id' struct_conn no '_struct_mon_nucl.auth_comp_id' struct_mon_nucl no '_struct_mon_prot.auth_comp_id' struct_mon_prot no '_struct_mon_prot_cis.auth_comp_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_comp_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_comp_id' struct_ncs_dom_lim no '_struct_sheet_range.beg_auth_comp_id' struct_sheet_range no '_struct_sheet_range.end_auth_comp_id' struct_sheet_range no '_struct_site_gen.auth_comp_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_angle.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_angle.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id' '_geom_bond.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_bond.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_contact.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_contact.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_A' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_D' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_H' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_4' '_atom_site.auth_comp_id' '_struct_conf.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conf.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conn.ptnr1_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conn.ptnr2_auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_nucl.auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_prot.auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_prot_cis.auth_comp_id' '_atom_site.auth_comp_id' '_struct_ncs_dom_lim.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_ncs_dom_lim.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_sheet_range.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_sheet_range.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_site_gen.auth_comp_id' '_atom_site.auth_comp_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_seq_id _item_description.description ; An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_seq_id' atom_site no '_geom_angle.atom_site_auth_seq_id_1' geom_angle no '_geom_angle.atom_site_auth_seq_id_2' geom_angle no '_geom_angle.atom_site_auth_seq_id_3' geom_angle no '_geom_bond.atom_site_auth_seq_id_1' geom_bond no '_geom_bond.atom_site_auth_seq_id_2' geom_bond no '_geom_contact.atom_site_auth_seq_id_1' geom_contact no '_geom_contact.atom_site_auth_seq_id_2' geom_contact no '_geom_hbond.atom_site_auth_seq_id_A' geom_hbond no '_geom_hbond.atom_site_auth_seq_id_D' geom_hbond no '_geom_hbond.atom_site_auth_seq_id_H' geom_hbond no '_geom_torsion.atom_site_auth_seq_id_1' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_2' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_3' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_4' geom_torsion no '_struct_conf.beg_auth_seq_id' struct_conf no '_struct_conf.end_auth_seq_id' struct_conf no '_struct_conn.ptnr1_auth_seq_id' struct_conn no '_struct_conn.ptnr2_auth_seq_id' struct_conn no '_struct_mon_nucl.auth_seq_id' struct_mon_nucl no '_struct_mon_prot.auth_seq_id' struct_mon_prot no '_struct_mon_prot_cis.auth_seq_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_seq_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_seq_id' struct_ncs_dom_lim no '_struct_sheet_hbond.range_1_beg_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_1_end_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_beg_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_end_auth_seq_id' struct_sheet_hbond no '_struct_sheet_range.beg_auth_seq_id' struct_sheet_range no '_struct_sheet_range.end_auth_seq_id' struct_sheet_range no '_struct_site_gen.auth_seq_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_angle.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_angle.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id' '_geom_bond.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_bond.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_contact.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_contact.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_A' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_D' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_H' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_4' '_atom_site.auth_seq_id' '_struct_conf.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conf.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conn.ptnr1_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conn.ptnr2_auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_nucl.auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_prot.auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_prot_cis.auth_seq_id' '_atom_site.auth_seq_id' '_struct_ncs_dom_lim.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_ncs_dom_lim.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_1_beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_1_end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_2_beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_2_end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_range.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_range.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_site_gen.auth_seq_id' '_atom_site.auth_seq_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.B_equiv_geom_mean _item_description.description ; Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.B_equiv_geom_mean' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_equiv_geom_mean' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_equiv_geom_mean_esd' associated_esd '_atom_site.U_equiv_geom_mean' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_equiv_geom_mean_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.B_equiv_geom_mean. ; _item.name '_atom_site.B_equiv_geom_mean_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_equiv_geom_mean' associated_value '_atom_site.U_equiv_geom_mean' conversion_constant _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_iso_or_equiv _item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.B_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_iso_or_equiv' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_iso_or_equiv_esd' associated_esd '_atom_site.U_iso_or_equiv' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_iso_or_equiv_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.B_iso_or_equiv. ; _item.name '_atom_site.B_iso_or_equiv_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_iso_or_equiv' associated_value '_atom_site.U_iso_or_equiv_esd' conversion_constant _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.calc_attached_atom _item_description.description ; The _atom_site.id of the atom site to which the 'geometry-calculated' atom site is attached. ; _item.name '_atom_site.calc_attached_atom' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_attached_atom' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__atom_site.calc_flag _item_description.description ; A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'. ; _item.name '_atom_site.calc_flag' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value d _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail d 'determined from experimental measurements' calc 'calculated from molecular geometry' c 'abbreviation for "calc"' dum 'dummy site with meaningless coordinates' save_ save__atom_site.Cartn_x _item_description.description ; The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y' '_atom_site.Cartn_z' _item_related.related_name '_atom_site.Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_x. ; _item.name '_atom_site.Cartn_x_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y_esd' '_atom_site.Cartn_z_esd' _item_related.related_name '_atom_site.Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.Cartn_y _item_description.description ; The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_z' _item_related.related_name '_atom_site.Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_y. ; _item.name '_atom_site.Cartn_y_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x_esd' '_atom_site.Cartn_z_esd' _item_related.related_name '_atom_site.Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.Cartn_z _item_description.description ; The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_y' _item_related.related_name '_atom_site.Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_z. ; _item.name '_atom_site.Cartn_z_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x_esd' '_atom_site.Cartn_y_esd' _item_related.related_name '_atom_site.Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.chemical_conn_number _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_atom_site.chemical_conn_number' _item.mandatory_code no _item_aliases.alias_name '_atom_site_chemical_conn_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site.constraints _item_description.description ; A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_constraints. ; _item.name '_atom_site.constraints' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_constraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'pop=1.0-pop(Zn3)' save_ save__atom_site.details _item_description.description ; A description of special aspects of this site. See also _atom_site.refinement_flags. ; _item.name '_atom_site.details' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Ag/Si disordered' save_ save__atom_site.disorder_assembly _item_description.description ; A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_site.disorder_assembly' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_disorder_assembly' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__atom_site.disorder_group _item_description.description ; A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_site.disorder_group' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_disorder_group' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value . _item_type.code code save_ save__atom_site.footnote_id _item_description.description ; The value of _atom_site.footnote_id must match an ID specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list. ; _item.name '_atom_site.footnote_id' _item.mandatory_code no save_ save__atom_site.fract_x _item_description.description ; The x coordinate of the atom-site position specified as a fraction of _cell.length_a. ; _item.name '_atom_site.fract_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.fract_y' '_atom_site.fract_z' _item_related.related_name '_atom_site.fract_x_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.fract_x. ; _item.name '_atom_site.fract_x_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_y_esd' '_atom_site.fract_z_esd' _item_related.related_name '_atom_site.fract_x' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.fract_y _item_description.description ; The y coordinate of the atom-site position specified as a fraction of _cell.length_b. ; _item.name '_atom_site.fract_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_z' _item_related.related_name '_atom_site.fract_y_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.fract_y. ; _item.name '_atom_site.fract_y_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_z_esd' _item_related.related_name '_atom_site.fract_y' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.fract_z _item_description.description ; The z coordinate of the atom-site position specified as a fraction of _cell.length_c. ; _item.name '_atom_site.fract_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_y' _item_related.related_name '_atom_site.fract_z_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.fract_z. ; _item.name '_atom_site.fract_z_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_y_esd' _item_related.related_name '_atom_site.fract_z' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.group_PDB _item_description.description ; The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_atom_site.group_PDB' _item.category_id atom_site _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value ATOM HETATM save_ save__atom_site.id _item_description.description ; The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and _atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to _atom_site.id. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.id' atom_site yes '_atom_site_anisotrop.id' atom_site_anisotrop yes '_geom_angle.atom_site_id_1' geom_angle yes '_geom_angle.atom_site_id_2' geom_angle yes '_geom_angle.atom_site_id_3' geom_angle yes '_geom_bond.atom_site_id_1' geom_bond yes '_geom_bond.atom_site_id_2' geom_bond yes '_geom_contact.atom_site_id_1' geom_contact yes '_geom_contact.atom_site_id_2' geom_contact yes '_geom_hbond.atom_site_id_A' geom_hbond yes '_geom_hbond.atom_site_id_D' geom_hbond yes '_geom_hbond.atom_site_id_H' geom_hbond yes '_geom_torsion.atom_site_id_1' geom_torsion yes '_geom_torsion.atom_site_id_2' geom_torsion yes '_geom_torsion.atom_site_id_3' geom_torsion yes '_geom_torsion.atom_site_id_4' geom_torsion yes _item_aliases.alias_name '_atom_site_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site_anisotrop.id' '_atom_site.id' '_geom_angle.atom_site_id_1' '_atom_site.id' '_geom_angle.atom_site_id_2' '_atom_site.id' '_geom_angle.atom_site_id_3' '_atom_site.id' '_geom_bond.atom_site_id_1' '_atom_site.id' '_geom_bond.atom_site_id_2' '_atom_site.id' '_geom_contact.atom_site_id_1' '_atom_site.id' '_geom_contact.atom_site_id_2' '_atom_site.id' '_geom_hbond.atom_site_id_A' '_atom_site.id' '_geom_hbond.atom_site_id_D' '_atom_site.id' '_geom_hbond.atom_site_id_H' '_atom_site.id' '_geom_torsion.atom_site_id_1' '_atom_site.id' '_geom_torsion.atom_site_id_2' '_atom_site.id' '_geom_torsion.atom_site_id_3' '_atom_site.id' '_geom_torsion.atom_site_id_4' '_atom_site.id' _item_type.code code loop_ _item_examples.case '5' 'C12' 'Ca3g28' 'Fe3+17' 'H*251' 'boron2a' 'C_a_phe_83_a_0' 'Zn_Zn_301_A_0' save_ save__atom_site.label_alt_id _item_description.description ; A component of the identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_atom_site.label_alt_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_asym_id _item_description.description ; A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_atom_site.label_asym_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_atom_id _item_description.description ; A component of the identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_atom_site.label_atom_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_comp_id _item_description.description ; A component of the identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_atom_site.label_comp_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_atom_site.label_entity_id' _item.mandatory_code yes save_ save__atom_site.label_seq_id _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_atom_site.label_seq_id' _item.mandatory_code yes save_ save__atom_site.occupancy _item_description.description ; The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_atom_site.occupancy' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_occupancy' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1.0 # JDW 17-Apr-2003 - Unsupportable restriction. # loop_ # _item_range.maximum # _item_range.minimum 1.0 1.0 # 1.0 0.0 # 0.0 0.0 _item_related.related_name '_atom_site.occupancy_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__atom_site.occupancy_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.occupancy. ; _item.name '_atom_site.occupancy_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_atom_site.occupancy' _item_related.function_code associated_value _item_type.code float save_ #save__atom_site.refinement_flags # _item_description.description #; A concatenated series of single-letter codes which indicate the # refinement restraints or constraints applied to this site. #; # _item.name '_atom_site.refinement_flags' # _item.category_id atom_site # _item.mandatory_code no # _item_aliases.alias_name '_atom_site_refinement_flags' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # _item_type.code ucode # loop_ # _item_enumeration.value # _item_enumeration.detail . # 'no refinement constraints' # S # 'special-position constraint on site' # G # 'rigid-group refinement of site' # R # 'riding atom site attached to non-riding atom' # D # 'distance or angle restraint on site' # T # 'thermal displacement constraints' # U # 'Uiso or Uij restraint (rigid bond)' # P # 'partial occupancy constraint' # save_ save__atom_site.restraints _item_description.description ; A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_restraints. ; _item.name '_atom_site.restraints' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_restraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'restrained to planar ring' save_ save__atom_site.symmetry_multiplicity _item_description.description ; The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002). ; _item.name '_atom_site.symmetry_multiplicity' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_symmetry_multiplicity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 192 192 192 1 1 1 _item_type.code int save_ save__atom_site.thermal_displace_type _item_description.description ; A standard code used to describe the type of atomic displacement parameters used for the site. ; _item.name '_atom_site.thermal_displace_type' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_thermal_displace_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' save_ save__atom_site.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site.U_equiv_geom_mean _item_description.description ; Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ ; _item.name '_atom_site.U_equiv_geom_mean' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_equiv_geom_mean' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 10.0 10.0 10.0 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_equiv_geom_mean_esd' associated_esd '_atom_site.B_equiv_geom_mean' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.U_equiv_geom_mean_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.U_equiv_geom_mean. ; _item.name '_atom_site.U_equiv_geom_mean_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_equiv_geom_mean' associated_value '_atom_site.B_equiv_geom_mean' conversion_constant _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.U_iso_or_equiv _item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. ; _item.name '_atom_site.U_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_iso_or_equiv' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 10.0 10.0 10.0 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_iso_or_equiv_esd' associated_esd '_atom_site.B_iso_or_equiv' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.U_iso_or_equiv_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site.U_iso_or_equiv. ; _item.name '_atom_site.U_iso_or_equiv_esd' _item.category_id atom_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_iso_or_equiv' associated_value '_atom_site.B_iso_or_equiv_esd' conversion_constant _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.Wyckoff_symbol _item_description.description ; The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002). ; _item.name '_atom_site.Wyckoff_symbol' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Wyckoff_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ######################### ## ATOM_SITE_ANISOTROP ## ######################### save_atom_site_anisotrop _category.description ; Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. ; _category.id atom_site_anisotrop _category.mandatory_code no _category_key.name '_atom_site_anisotrop.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [Acta Cryst. (1985), B41, 255-262]. ; ; loop_ _atom_site_anisotrop.id _atom_site_anisotrop.type_symbol _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[1][2] _atom_site_anisotrop.U[1][3] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[2][3] _atom_site_anisotrop.U[3][3] 1 O 8642 4866 7299 -342 -258 -1427 2 C 5174 4871 6243 -1885 -2051 -1377 3 C 6202 5020 4395 -1130 -556 -632 4 O 4224 4700 5046 1105 -161 345 5 C 8684 4688 4171 -1850 -433 -292 6 O 11226 5255 3532 -341 2685 1328 7 C 10214 2428 5614 -2610 -1940 902 8 C 4590 3488 5827 751 -770 986 9 N 5014 4434 3447 -17 -1593 539 # ---- abbreviated ---- ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_site_anisotrop.B[1][1] _item_description.description ; The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][1]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][1]_esd' associated_esd '_atom_site.aniso_U[1][1]' conversion_constant '_atom_site_anisotrop.U[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][1]. ; _item.name '_atom_site_anisotrop.B[1][1]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][1]' associated_value '_atom_site.aniso_U[1][1]_esd' conversion_constant '_atom_site_anisotrop.U[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][2] _item_description.description ; The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][2]_esd' associated_esd '_atom_site.aniso_U[1][2]' conversion_constant '_atom_site_anisotrop.U[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][2]. ; _item.name '_atom_site_anisotrop.B[1][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][2]' associated_value '_atom_site.aniso_U[1][2]_esd' conversion_constant '_atom_site_anisotrop.U[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][3] _item_description.description ; The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][3]_esd' associated_esd '_atom_site.aniso_U[1][3]' conversion_constant '_atom_site_anisotrop.U[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][3]. ; _item.name '_atom_site_anisotrop.B[1][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][3]' associated_value '_atom_site.aniso_U[1][3]_esd' conversion_constant '_atom_site_anisotrop.U[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][2] _item_description.description ; The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[2][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][2]_esd' associated_esd '_atom_site.aniso_U[2][2]' conversion_constant '_atom_site_anisotrop.U[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[2][2]. ; _item.name '_atom_site_anisotrop.B[2][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][2]' associated_value '_atom_site.aniso_U[2][2]_esd' conversion_constant '_atom_site_anisotrop.U[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][3] _item_description.description ; The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[2][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][3]_esd' associated_esd '_atom_site.aniso_U[2][3]' conversion_constant '_atom_site_anisotrop.U[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[2][3]. ; _item.name '_atom_site_anisotrop.B[2][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][3]' associated_value '_atom_site.aniso_U[2][3]_esd' conversion_constant '_atom_site_anisotrop.U[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[3][3] _item_description.description ; The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[3][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[3][3]_esd' associated_esd '_atom_site.aniso_U[3][3]' conversion_constant '_atom_site_anisotrop.U[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[3][3]. ; _item.name '_atom_site_anisotrop.B[3][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[3][3]' associated_value '_atom_site.aniso_U[3][3]_esd' conversion_constant '_atom_site_anisotrop.U[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.ratio _item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site_anisotrop.ratio' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_ratio' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_related.related_name '_atom_site.aniso_ratio' _item_related.function_code alternate_exclusive _item_type.code float save_ save__atom_site_anisotrop.id _item_description.description ; This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_atom_site_anisotrop.id' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_aniso_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site_anisotrop.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site_anisotrop.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_aniso_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site_anisotrop.U[1][1] _item_description.description ; The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][1]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][1]_esd' associated_esd '_atom_site.aniso_B[1][1]' conversion_constant '_atom_site_anisotrop.B[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][1]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][1]. ; _item.name '_atom_site_anisotrop.U[1][1]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][1]' associated_value '_atom_site.aniso_B[1][1]_esd' conversion_constant '_atom_site_anisotrop.B[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][2] _item_description.description ; The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][2]_esd' associated_esd '_atom_site.aniso_B[1][2]' conversion_constant '_atom_site_anisotrop.B[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][2]. ; _item.name '_atom_site_anisotrop.U[1][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][2]' associated_value '_atom_site.aniso_B[1][2]_esd' conversion_constant '_atom_site_anisotrop.B[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][3] _item_description.description ; The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][3]_esd' associated_esd '_atom_site.aniso_B[1][3]' conversion_constant '_atom_site_anisotrop.B[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][3]. ; _item.name '_atom_site_anisotrop.U[1][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][3]' associated_value '_atom_site.aniso_B[1][3]_esd' conversion_constant '_atom_site_anisotrop.B[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][2] _item_description.description ; The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[2][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][2]_esd' associated_esd '_atom_site.aniso_B[2][2]' conversion_constant '_atom_site_anisotrop.B[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][2]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[2][2]. ; _item.name '_atom_site_anisotrop.U[2][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][2]' associated_value '_atom_site.aniso_B[2][2]_esd' conversion_constant '_atom_site_anisotrop.B[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][3] _item_description.description ; The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[2][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][3]_esd' associated_esd '_atom_site.aniso_B[2][3]' conversion_constant '_atom_site_anisotrop.B[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[2][3]. ; _item.name '_atom_site_anisotrop.U[2][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][3]' associated_value '_atom_site.aniso_B[2][3]_esd' conversion_constant '_atom_site_anisotrop.B[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[3][3] _item_description.description ; The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[3][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[3][3]_esd' associated_esd '_atom_site.aniso_B[3][3]' conversion_constant '_atom_site_anisotrop.B[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[3][3]_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[3][3]. ; _item.name '_atom_site_anisotrop.U[3][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no # _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[3][3]' associated_value '_atom_site.aniso_B[3][3]_esd' conversion_constant '_atom_site_anisotrop.B[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive _item_type.code float _item_units.code angstroms_squared save_ ################ ## ATOM_SITES ## ################ save_atom_sites _category.description ; Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. ; _category.id atom_sites _category.mandatory_code no _category_key.name '_atom_sites.entry_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _atom_sites.entry_id '5HVP' _atom_sites.Cartn_transform_axes 'c along z, astar along x, b along y' _atom_sites.Cartn_transf_matrix[1][1] 58.39 _atom_sites.Cartn_transf_matrix[1][2] 0.00 _atom_sites.Cartn_transf_matrix[1][3] 0.00 _atom_sites.Cartn_transf_matrix[2][1] 0.00 _atom_sites.Cartn_transf_matrix[2][2] 86.70 _atom_sites.Cartn_transf_matrix[2][3] 0.00 _atom_sites.Cartn_transf_matrix[3][1] 0.00 _atom_sites.Cartn_transf_matrix[3][2] 0.00 _atom_sites.Cartn_transf_matrix[3][3] 46.27 _atom_sites.Cartn_transf_vector[1] 0.00 _atom_sites.Cartn_transf_vector[2] 0.00 _atom_sites.Cartn_transf_vector[3] 0.00 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_atom_sites.entry_id' _item.mandatory_code yes save_ save__atom_sites.Cartn_transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_vector[1] _item_description.description ; The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transf_vector[2] _item_description.description ; The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transf_vector[3] _item_description.description ; The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transform_axes _item_description.description ; A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix[][]. ; _item.name '_atom_sites.Cartn_transform_axes' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_transform_axes' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'a parallel to x; b in the plane of y and z' save_ save__atom_sites.fract_transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_vector[1] _item_description.description ; The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.fract_transf_vector[2] _item_description.description ; The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.fract_transf_vector[3] _item_description.description ; The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.solution_primary _item_description.description ; This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_primary' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_primary' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ save__atom_sites.solution_secondary _item_description.description ; This code identifies the method used to locate the non-hydrogen-atom sites not found by _atom_sites.solution_primary. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_secondary' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_secondary' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ save__atom_sites.solution_hydrogens _item_description.description ; This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_hydrogens' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_hydrogens' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ #################### ## ATOM_SITES_ALT ## #################### save_atom_sites_alt _category.description ; Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block. ; _category.id atom_sites_alt _category.mandatory_code no _category_key.name '_atom_sites_alt.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_alt.id _atom_sites_alt.details . ; Atom sites with the alternative ID set to null are not modeled in alternative conformations ; 1 ; Atom sites with the alternative ID set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 2. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 1 correlate with the conformation of the inhibitor marked with alternative ID 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor. ; 2 ; Atom sites with the alternative ID set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 1. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 2 correlate with the conformation of the inhibitor marked with alternative ID 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor. ; 3 ; Atom sites with the alternative ID set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative ID 4. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; 4 ; Atom sites with the alternative ID set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative ID 3. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt.details _item_description.description ; A description of special aspects of the modelling of atoms in alternative conformations. ; _item.name '_atom_sites_alt.details' _item.category_id atom_sites_alt _item.mandatory_code no _item_type.code text save_ save__atom_sites_alt.id _item_description.description ; The value of _atom_sites_alt.id must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt.id' atom_sites_alt yes '_atom_site.label_alt_id' atom_site no '_atom_sites_alt_gen.alt_id' atom_sites_alt_gen yes '_geom_angle.atom_site_label_alt_id_1' geom_angle no '_geom_angle.atom_site_label_alt_id_2' geom_angle no '_geom_angle.atom_site_label_alt_id_3' geom_angle no '_geom_bond.atom_site_label_alt_id_1' geom_bond no '_geom_bond.atom_site_label_alt_id_2' geom_bond no '_geom_contact.atom_site_label_alt_id_1' geom_contact no '_geom_contact.atom_site_label_alt_id_2' geom_contact no '_geom_hbond.atom_site_label_alt_id_A' geom_hbond no '_geom_hbond.atom_site_label_alt_id_D' geom_hbond no '_geom_hbond.atom_site_label_alt_id_H' geom_hbond no '_geom_torsion.atom_site_label_alt_id_1' geom_torsion no '_geom_torsion.atom_site_label_alt_id_2' geom_torsion no '_geom_torsion.atom_site_label_alt_id_3' geom_torsion no '_geom_torsion.atom_site_label_alt_id_4' geom_torsion no '_struct_conn.ptnr1_label_alt_id' struct_conn no '_struct_conn.ptnr2_label_alt_id' struct_conn no '_struct_mon_nucl.label_alt_id' struct_mon_nucl yes '_struct_mon_prot.label_alt_id' struct_mon_prot yes '_struct_mon_prot_cis.label_alt_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_alt_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_alt_id' struct_ncs_dom_lim yes '_struct_site_gen.label_alt_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_alt_id' '_atom_sites_alt.id' '_atom_sites_alt_gen.alt_id' '_atom_sites_alt.id' '_geom_angle.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_angle.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_angle.atom_site_label_alt_id_3' '_atom_site.label_alt_id' '_geom_bond.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_bond.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_contact.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_contact.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_A' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_D' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_H' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_3' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_4' '_atom_site.label_alt_id' '_struct_conn.ptnr1_label_alt_id' '_atom_site.label_alt_id' '_struct_conn.ptnr2_label_alt_id' '_atom_site.label_alt_id' '_struct_mon_nucl.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot_cis.label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_lim.beg_label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_lim.end_label_alt_id' '_atom_site.label_alt_id' '_struct_site_gen.label_alt_id' '_atom_site.label_alt_id' _item_type.code code loop_ _item_examples.case 'orientation 1' 'molecule abc' save_ ######################## ## ATOM_SITES_ALT_ENS ## ######################## save_atom_sites_alt_ens _category.description ; Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs. ; _category.id atom_sites_alt_ens _category.mandatory_code no _category_key.name '_atom_sites_alt_ens.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_alt_ens.id _atom_sites_alt_ens.details 'Ensemble 1-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 1-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt_ens.details _item_description.description ; A description of special aspects of the ensemble structure generated from atoms with various alternative IDs. ; _item.name '_atom_sites_alt_ens.details' _item.category_id atom_sites_alt_ens _item.mandatory_code no _item_type.code text save_ save__atom_sites_alt_ens.id _item_description.description ; The value of _atom_sites_alt_ens.id must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt_ens.id' atom_sites_alt_ens yes '_atom_sites_alt_gen.ens_id' atom_sites_alt_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_ens.id' _item_type.code code save_ ######################## ## ATOM_SITES_ALT_GEN ## ######################## save_atom_sites_alt_gen _category.description ; Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. ; _category.id atom_sites_alt_gen _category.mandatory_code no loop_ _category_key.name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_gen.alt_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_alt_gen.ens_id _atom_sites_alt_gen.alt_id 'Ensemble 1-A' . 'Ensemble 1-A' 1 'Ensemble 1-A' 3 'Ensemble 1-B' . 'Ensemble 1-B' 1 'Ensemble 1-B' 4 'Ensemble 2-A' . 'Ensemble 2-A' 2 'Ensemble 2-A' 3 'Ensemble 2-B' . 'Ensemble 2-B' 2 'Ensemble 2-B' 4 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt_gen.alt_id _item_description.description ; This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_atom_sites_alt_gen.alt_id' _item.mandatory_code yes save_ save__atom_sites_alt_gen.ens_id _item_description.description ; This data item is a pointer to _atom_sites_alt_ens.id in the ATOM_SITES_ALT_ENS category. ; _item.name '_atom_sites_alt_gen.ens_id' _item.mandatory_code yes save_ ######################### ## ATOM_SITES_FOOTNOTE ## ######################### save_atom_sites_footnote _category.description ; Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites. ; _category.id atom_sites_footnote _category.mandatory_code no _category_key.name '_atom_sites_footnote.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_sites_footnote.id _atom_sites_footnote.text 1 ; The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative IDs *1* and *2*. ; 2 ; Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 3 ; The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 4 ; Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor. ; 5 ; The positions of these water molecules correlate with alternative orientations of amino-acid side chains that do not correlate with alternative orientations of the inhibitor. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_footnote.id _item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case 'a' 'b' '1' '2' save_ save__atom_sites_footnote.text _item_description.description ; The text of the footnote. Footnotes are used to describe an atom site or a group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled. ; _item.name '_atom_sites_footnote.text' _item.category_id atom_sites_footnote _item.mandatory_code no _item_type.code text save_ ############### ## ATOM_TYPE ## ############### save_atom_type _category.description ; Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors. ; _category.id atom_type _category.mandatory_code no _category_key.name '_atom_type.symbol' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c C 0 2.31000 20.8439 1.02000 10.2075 1.58860 0.568700 0.865000 51.6512 0.21560 N 0 12.2126 0.005700 3.13220 9.89330 2.01250 28.9975 1.16630 0.582600 -11.529 O 0 3.04850 13.2771 2.28680 5.70110 1.54630 0.323900 0.867000 32.9089 0.250800 S 0 6.90530 1.46790 5.20340 22.2151 1.43790 0.253600 1.58630 56.1720 0.866900 CL -1 18.2915 0.006600 7.20840 1.17170 6.53370 19.5424 2.33860 60.4486 -16.378 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.number_in_cell _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_source C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_type.analytical_mass_percent _item_description.description ; Mass percentage of this atom type derived from chemical analysis. ; _item.name '_atom_type.analytical_mass_percent' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_analytical_mass_%' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__atom_type.description _item_description.description ; A description of the atom(s) designated by this atom type. In most cases, this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. ; _item.name '_atom_type.description' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'deuterium' '0.34Fe+0.66Ni' save_ save__atom_type.number_in_cell _item_description.description ; Total number of atoms of this atom type in the unit cell. ; _item.name '_atom_type.number_in_cell' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_number_in_cell' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__atom_type.oxidation_number _item_description.description ; Formal oxidation state of this atom type in the structure. ; _item.name '_atom_type.oxidation_number' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_oxidation_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int save_ save__atom_type.radius_bond _item_description.description ; The effective intramolecular bonding radius in angstroms of this atom type. ; _item.name '_atom_type.radius_bond' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_bond' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 5.0 5.0 5.0 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__atom_type.radius_contact _item_description.description ; The effective intermolecular bonding radius in angstroms of this atom type. ; _item.name '_atom_type.radius_contact' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_contact' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 5.0 5.0 5.0 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__atom_type.scat_Cromer_Mann_a1 _item_description.description ; The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a1' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a2 _item_description.description ; The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a2' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a3 _item_description.description ; The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a3' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a4 _item_description.description ; The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a4' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b1 _item_description.description ; The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b1' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b2 _item_description.description ; The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b2' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b3 _item_description.description ; The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b3' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b4 _item_description.description ; The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b4' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_c _item_description.description ; The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_c' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_c' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' _item_type.code float save_ save__atom_type.scat_dispersion_imag _item_description.description ; The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id. ; _item.name '_atom_type.scat_dispersion_imag' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_imag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_real' _item_type.code float save_ save__atom_type.scat_dispersion_real _item_description.description ; The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id. ; _item.name '_atom_type.scat_dispersion_real' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_real' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_imag' _item_type.code float save_ save__atom_type.scat_length_neutron _item_description.description ; The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. ; _item.name '_atom_type.scat_length_neutron' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_length_neutron' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_units.code femtometres save_ save__atom_type.scat_source _item_description.description ; Reference to the source of the scattering factors or scattering lengths used for this atom type. ; _item.name '_atom_type.scat_source' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_source' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'International Tables Vol. IV Table 2.4.6B' save_ save__atom_type.scat_versus_stol_list _item_description.description ; A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. ; _item.name '_atom_type.scat_versus_stol_list' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_versus_stol_list' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__atom_type.symbol _item_description.description ; The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes '_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes '_chemical_conn_atom.type_symbol' chemical_conn_atom yes '_chem_comp_atom.type_symbol' chem_comp_atom yes '_phasing_MIR_der_site.atom_type_symbol' phasing_MIR_der_site yes _item_aliases.alias_name '_atom_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.type_symbol' '_atom_type.symbol' '_atom_site_anisotrop.type_symbol' '_atom_type.symbol' '_chemical_conn_atom.type_symbol' '_atom_type.symbol' '_chem_comp_atom.type_symbol' '_atom_type.symbol' '_phasing_MIR_der_site.atom_type_symbol' '_atom_type.symbol' _item_type.code code loop_ _item_examples.case 'C' 'Cu2+' 'H(SDS)' 'dummy' 'FeNi' save_ ########### ## AUDIT ## ########### save_audit _category.description ; Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block. ; _category.id audit _category.mandatory_code no _category_key.name '_audit.revision_id' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _audit.revision_id 1 _audit.creation_date '1992-12-08' _audit.creation_method ; Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records ; _audit.update_record ; 1992-12-09 adjusted to reflect comments from B. McKeever 1992-12-10 adjusted to reflect comments from H. Berman 1992-12-12 adjusted to reflect comments from K. Watenpaugh ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _audit.creation_date 1991-03-20 _audit.creation_method from_xtal_archive_file_using_CIFIO _audit.update_record ; 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec'd by co-editor as manuscript HL0007. 1991-04-17 adjustments based on first referee report. 1991-04-18 adjustments based on second referee report. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit.creation_date _item_description.description ; A date that the data block was created. The date format is yyyy-mm-dd. ; _item.name '_audit.creation_date' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_creation_date' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd _item_examples.case '1990-07-12' save_ save__audit.creation_method _item_description.description ; A description of how data were entered into the data block. ; _item.name '_audit.creation_method' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_creation_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'spawned by the program QBEE' save_ save__audit.revision_id _item_description.description ; The value of _audit.revision_id must uniquely identify a record in the AUDIT list. ; _item.name '_audit.revision_id' _item.category_id audit _item.mandatory_code yes _item_type.code code _item_examples.case 'rev1' save_ save__audit.update_record _item_description.description ; A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. ; _item.name '_audit.update_record' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_update_record' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '1990-07-15 Updated by the Co-editor' save_ ################## ## AUDIT_AUTHOR ## ################## save_audit_author _category.description ; Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. ; _category.id audit_author _category.mandatory_code no _category_key.name '_audit_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _audit_author.name _audit_author.address 'Fitzgerald, Paula M.D.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'McKeever, Brian M.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Van Middlesworth, J.F.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Springer, James P.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_author.address _item_description.description ; The address of an author of this data block. If there are multiple authors, _audit_author.address is looped with _audit_author.name. ; _item.name '_audit_author.address' _item.category_id audit_author _item.mandatory_code no _item_aliases.alias_name '_audit_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__audit_author.name _item_description.description ; The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_audit_author.name' _item.category_id audit_author _item.mandatory_code yes _item_aliases.alias_name '_audit_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' save_ ################### ## AUDIT_CONFORM ## ################### save_audit_conform _category.description ; Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. ; _category.id audit_conform _category.mandatory_code no loop_ _category_key.name '_audit_conform.dict_name' '_audit_conform.dict_version' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - any file conforming to the current CIF core dictionary. ; ; _audit_conform.dict_name cif_core.dic _audit_conform.dict_version 2.3.1 _audit_conform.dict_location ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_conform.dict_location _item_description.description ; A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. ; _item.name '_audit_conform.dict_location' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_location' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__audit_conform.dict_name _item_description.description ; The string identifying the highest-level dictionary defining data names used in this file. ; _item.name '_audit_conform.dict_name' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__audit_conform.dict_version _item_description.description ; The version number of the dictionary to which the current data block conforms. ; _item.name '_audit_conform.dict_version' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_version' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ########################## ## AUDIT_CONTACT_AUTHOR ## ########################## save_audit_contact_author _category.description ; Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block. ; _category.id audit_contact_author _category.mandatory_code no _category_key.name '_audit_contact_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _audit_contact_author.name 'Fitzgerald, Paula M.D.' _audit_contact_author.address ; Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; _audit_contact_author.phone '1(908)5945510' _audit_contact_author.fax '1(908)5946645' _audit_contact_author.email 'paula_fitzgerald@merck.com' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_contact_author.address _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed. ; _item.name '_audit_contact_author.address' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__audit_contact_author.email _item_description.description ; The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; _item.name '_audit_contact_author.email' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'name@host.domain.country' 'bm@iucr.org' save_ save__audit_contact_author.fax _item_description.description ; The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. ; _item.name '_audit_contact_author.fax' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477334' '12()349477334' save_ save__audit_contact_author.name _item_description.description ; The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_audit_contact_author.name' _item.category_id audit_contact_author _item.mandatory_code yes _item_aliases.alias_name '_audit_contact_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' save_ save__audit_contact_author.phone _item_description.description ; The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. ; _item.name '_audit_contact_author.phone' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' '12(34)9477330x5543' save_ ########## ## CELL ## ########## save_cell _category.description ; Data items in the CELL category record details about the crystallographic cell parameters. ; _category.id cell _category.mandatory_code no _category_key.name '_cell.entry_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _cell.entry_id '5HVP' _cell.length_a 58.39 _cell.length_a_esd 0.05 _cell.length_b 86.70 _cell.length_b_esd 0.12 _cell.length_c 46.27 _cell.length_c_esd 0.06 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.volume 234237 _cell.details ; The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _cell.length_a 5.959 _cell.length_a_esd 0.001 _cell.length_b 14.956 _cell.length_b_esd 0.001 _cell.length_c 19.737 _cell.length_c_esd 0.003 _cell.angle_alpha 90.0 _cell.angle_beta 90.0 _cell.angle_gamma 90.0 _cell.volume 1759.0 _cell.volume_esd 0.3 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell.angle_alpha _item_description.description ; Unit-cell angle alpha of the reported structure in degrees. ; _item.name '_cell.angle_alpha' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_alpha' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_beta' '_cell.angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_alpha_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_alpha_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.angle_alpha. ; _item.name '_cell.angle_alpha_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_beta_esd' '_cell.angle_gamma_esd' _item_related.related_name '_cell.angle_alpha' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.angle_beta _item_description.description ; Unit-cell angle beta of the reported structure in degrees. ; _item.name '_cell.angle_beta' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_beta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_beta_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_beta_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.angle_beta. ; _item.name '_cell.angle_beta_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_gamma_esd' _item_related.related_name '_cell.angle_beta' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.angle_gamma _item_description.description ; Unit-cell angle gamma of the reported structure in degrees. ; _item.name '_cell.angle_gamma' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_gamma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_beta' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_gamma_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_gamma_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.angle_gamma. ; _item.name '_cell.angle_gamma_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_beta_esd' _item_related.related_name '_cell.angle_gamma' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_cell.entry_id' _item.mandatory_code yes save_ save__cell.details _item_description.description ; A description of special aspects of the cell choice, noting possible alternative settings. ; _item.name '_cell.details' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'pseudo-orthorhombic' 'standard setting from 45 deg rotation around c' save_ save__cell.formula_units_Z _item_description.description ; The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum. ; _item.name '_cell.formula_units_Z' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_formula_units_Z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__cell.length_a _item_description.description ; Unit-cell length a corresponding to the structure reported in angstroms. ; _item.name '_cell.length_a' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_a' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_a_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_a_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.length_a. ; _item.name '_cell.length_a_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_b_esd' '_cell.length_c_esd' _item_related.related_name '_cell.length_a' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.length_b _item_description.description ; Unit-cell length b corresponding to the structure reported in angstroms. ; _item.name '_cell.length_b' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_b' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_b_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_b_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.length_b. ; _item.name '_cell.length_b_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_c_esd' _item_related.related_name '_cell.length_b' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.length_c _item_description.description ; Unit-cell length c corresponding to the structure reported in angstroms. ; _item.name '_cell.length_c' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_c' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_b' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_c_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_c_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.length_c. ; _item.name '_cell.length_c_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_b_esd' _item_related.related_name '_cell.length_c' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.volume _item_description.description ; Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = _cell.length_a b = _cell.length_b c = _cell.length_c alpha = _cell.angle_alpha beta = _cell.angle_beta gamma = _cell.angle_gamma ; _item.name '_cell.volume' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.volume_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__cell.volume_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell.volume. ; _item.name '_cell.volume_esd' _item.category_id cell _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_cell.volume' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ save__cell.Z_PDB _item_description.description ; The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_cell.Z_PDB' _item.category_id cell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ ###################### ## CELL_MEASUREMENT ## ###################### save_cell_measurement _category.description ; Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. ; _category.id cell_measurement _category.mandatory_code no _category_key.name '_cell_measurement.entry_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _cell_measurement.entry_id '5HVP' _cell_measurement.temp 293 _cell_measurement.temp_esd 3 _cell_measurement.theta_min 11 _cell_measurement.theta_max 31 _cell_measurement.wavelength 1.54 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _cell_measurement.temp 293 _cell_measurement.reflns_used 25 _cell_measurement.theta_min 25 _cell_measurement.theta_max 31 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell_measurement.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_cell_measurement.entry_id' _item.mandatory_code yes save_ save__cell_measurement.pressure _item_description.description ; The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). ; _item.name '_cell_measurement.pressure' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_pressure' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_cell_measurement.pressure_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kilopascals save_ save__cell_measurement.pressure_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell_measurement.pressure. ; _item.name '_cell_measurement.pressure_esd' _item.category_id cell_measurement _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_cell_measurement.pressure' _item_related.function_code associated_value _item_type.code float _item_units.code kilopascals save_ save__cell_measurement.radiation _item_description.description ; Description of the radiation used to measure the unit-cell data. See also _cell_measurement.wavelength. ; _item.name '_cell_measurement.radiation' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_radiation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'neutron' 'Cu K\a' 'synchrotron' save_ save__cell_measurement.reflns_used _item_description.description ; The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. ; _item.name '_cell_measurement.reflns_used' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_reflns_used' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__cell_measurement.temp _item_description.description ; The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). ; _item.name '_cell_measurement.temp' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_temperature' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell_measurement.temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvins save_ save__cell_measurement.temp_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _cell_measurement.temp. ; _item.name '_cell_measurement.temp_esd' _item.category_id cell_measurement _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_cell_measurement.temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvins save_ save__cell_measurement.theta_max _item_description.description ; The maximum theta angle of reflections used to measure the unit cell in degrees. ; _item.name '_cell_measurement.theta_max' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__cell_measurement.theta_min _item_description.description ; The minimum theta angle of reflections used to measure the unit cell in degrees. ; _item.name '_cell_measurement.theta_min' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__cell_measurement.wavelength _item_description.description ; The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH. ; _item.name '_cell_measurement.wavelength' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ ############################ ## CELL_MEASUREMENT_REFLN ## ############################ save_cell_measurement_refln _category.description ; Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. ; _category.id cell_measurement_refln _category.mandatory_code no loop_ _category_key.name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (unpublished). ; ; loop_ _cell_measurement_refln.index_h _cell_measurement_refln.index_k _cell_measurement_refln.index_l _cell_measurement_refln.theta -2 4 1 8.67 0 3 2 9.45 3 0 2 9.46 -3 4 1 8.93 -2 1 -2 7.53 10 0 0 23.77 0 10 0 23.78 -5 4 1 11.14 # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell_measurement_refln.index_h _item_description.description ; Miller index h of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_h' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.index_k _item_description.description ; Miller index k of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_k' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.index_l _item_description.description ; Miller index l of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_l' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.theta _item_description.description ; Theta angle for a reflection used for measurement of the unit cell in degrees. ; _item.name '_cell_measurement_refln.theta' _item.category_id cell_measurement_refln _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_refln_theta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ ############### ## CHEM_COMP ## ############### save_chem_comp _category.description ; Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components. ; _category.id chem_comp _category.mandatory_code no _category_key.name '_chem_comp.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp.id _chem_comp.model_source _chem_comp.name phe '1987 Protin/Prolsq Ideals file' phenylalanine val '1987 Protin/Prolsq Ideals file' alanine # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp.formula _item_description.description ; The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. ; _item.name '_chem_comp.formula' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chem_comp.formula_weight _item_description.description ; Formula mass in daltons of the chemical component. ; _item.name '_chem_comp.formula_weight' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chem_comp.id _item_description.description ; The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.id' chem_comp yes '_atom_site.label_comp_id' atom_site no '_chem_comp.mon_nstd_parent_comp_id' chem_comp no '_chem_comp_atom.comp_id' chem_comp_atom yes '_chem_comp_angle.comp_id' chem_comp_angle yes '_chem_comp_bond.comp_id' chem_comp_bond yes '_chem_comp_chir.comp_id' chem_comp_chir yes '_chem_comp_chir_atom.comp_id' chem_comp_chir_atom yes '_chem_comp_plane.comp_id' chem_comp_plane yes '_chem_comp_plane_atom.comp_id' chem_comp_plane_atom yes '_chem_comp_tor.comp_id' chem_comp_tor yes '_chem_comp_tor_value.comp_id' chem_comp_tor_value yes '_entity_poly_seq.mon_id' entity_poly_seq yes '_geom_angle.atom_site_label_comp_id_1' geom_angle no '_geom_angle.atom_site_label_comp_id_2' geom_angle no '_geom_angle.atom_site_label_comp_id_3' geom_angle no '_geom_bond.atom_site_label_comp_id_1' geom_bond no '_geom_bond.atom_site_label_comp_id_2' geom_bond no '_geom_contact.atom_site_label_comp_id_1' geom_contact no '_geom_contact.atom_site_label_comp_id_2' geom_contact no '_geom_hbond.atom_site_label_comp_id_A' geom_hbond no '_geom_hbond.atom_site_label_comp_id_D' geom_hbond no '_geom_hbond.atom_site_label_comp_id_H' geom_hbond no '_geom_torsion.atom_site_label_comp_id_1' geom_torsion no '_geom_torsion.atom_site_label_comp_id_2' geom_torsion no '_geom_torsion.atom_site_label_comp_id_3' geom_torsion no '_geom_torsion.atom_site_label_comp_id_4' geom_torsion no '_struct_conf.beg_label_comp_id' struct_conf yes '_struct_conf.end_label_comp_id' struct_conf yes '_struct_conn.ptnr1_label_comp_id' struct_conn yes '_struct_conn.ptnr2_label_comp_id' struct_conn yes '_struct_mon_nucl.label_comp_id' struct_mon_nucl yes '_struct_mon_prot.label_comp_id' struct_mon_prot yes '_struct_mon_prot_cis.label_comp_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_comp_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_comp_id' struct_ncs_dom_lim yes '_struct_ref_seq_dif.db_mon_id' struct_ref_seq_dif yes '_struct_ref_seq_dif.mon_id' struct_ref_seq_dif yes '_struct_sheet_range.beg_label_comp_id' struct_sheet_range yes '_struct_sheet_range.end_label_comp_id' struct_sheet_range yes '_struct_site_gen.label_comp_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_comp_id' '_chem_comp.id' '_chem_comp.mon_nstd_parent_comp_id' '_chem_comp.id' '_chem_comp_atom.comp_id' '_chem_comp.id' '_chem_comp_chir.comp_id' '_chem_comp.id' '_chem_comp_chir_atom.comp_id' '_chem_comp.id' '_chem_comp_plane.comp_id' '_chem_comp.id' '_chem_comp_plane_atom.comp_id' '_chem_comp.id' '_entity_poly_seq.mon_id' '_chem_comp.id' '_chem_comp_angle.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_bond.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_tor.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_tor_value.comp_id' '_chem_comp_atom.comp_id' '_geom_angle.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_angle.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_angle.atom_site_label_comp_id_3' '_atom_site.label_comp_id' '_geom_bond.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_bond.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_contact.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_contact.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_A' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_D' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_H' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_3' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_4' '_atom_site.label_comp_id' '_struct_conf.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_conf.end_label_comp_id' '_atom_site.label_comp_id' '_struct_conn.ptnr1_label_comp_id' '_atom_site.label_comp_id' '_struct_conn.ptnr2_label_comp_id' '_atom_site.label_comp_id' '_struct_mon_nucl.label_comp_id' '_atom_site.label_comp_id' '_struct_mon_prot.label_comp_id' '_atom_site.label_comp_id' '_struct_mon_prot_cis.label_comp_id' '_atom_site.label_comp_id' '_struct_ncs_dom_lim.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_ncs_dom_lim.end_label_comp_id' '_atom_site.label_comp_id' '_struct_ref_seq_dif.db_mon_id' '_chem_comp.id' '_struct_ref_seq_dif.mon_id' '_chem_comp.id' '_struct_sheet_range.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_sheet_range.end_label_comp_id' '_atom_site.label_comp_id' '_struct_site_gen.label_comp_id' '_atom_site.label_comp_id' _item_type.code ucode loop_ _item_examples.case 'ala' 'val' 'A' 'C' save_ save__chem_comp.model_details _item_description.description ; A description of special aspects of the generation of the coordinates for the model of the component. ; _item.name '_chem_comp.model_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code text _item_examples.case 'geometry idealized but not minimized' save_ save__chem_comp.model_erf _item_description.description ; A pointer to an external reference file from which the atomic description of the component is taken. ; _item.name '_chem_comp.model_erf' _item.category_id chem_comp _item.mandatory_code no _item_type.code line save_ save__chem_comp.model_source _item_description.description ; The source of the coordinates for the model of the component. ; _item.name '_chem_comp.model_source' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CSD entry ABCDEF' 'built using Quanta/Charmm' save_ save__chem_comp.mon_nstd_class _item_description.description ; A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer. ; _item.name '_chem_comp.mon_nstd_class' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'iodinated base' 'phosphorylated amino acid' 'brominated base' 'modified amino acid' 'glycosylated amino acid' save_ save__chem_comp.mon_nstd_details _item_description.description ; A description of special details of a nonstandard monomer. ; _item.name '_chem_comp.mon_nstd_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code text save_ save__chem_comp.mon_nstd_flag _item_description.description ; 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and _chem_comp.mon_nstd_details data items. ; _item.name '_chem_comp.mon_nstd_flag' _item.category_id chem_comp _item.mandatory_code no _item_type.code ucode _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail no 'the monomer is nonstandard' n 'abbreviation for "no"' yes 'the monomer is standard' y 'abbreviation for "yes"' save_ save__chem_comp.mon_nstd_parent _item_description.description ; The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. ; _item.name '_chem_comp.mon_nstd_parent' _item.category_id chem_comp _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'tyrosine' 'cytosine' save_ save__chem_comp.mon_nstd_parent_comp_id _item_description.description ; The identifier for the parent component of the nonstandard component. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp.mon_nstd_parent_comp_id' _item.mandatory_code no save_ save__chem_comp.name _item_description.description ; The full name of the component. ; _item.name '_chem_comp.name' _item.category_id chem_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'alanine' 'valine' 'adenine' 'cytosine' save_ save__chem_comp.number_atoms_all _item_description.description ; The total number of atoms in the component. ; _item.name '_chem_comp.number_atoms_all' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chem_comp.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the component. ; _item.name '_chem_comp.number_atoms_nh' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chem_comp.one_letter_code _item_description.description ; For standard polymer components, the one-letter code for the component. If there is not a standard one-letter code for this component, or if this is a non-polymer component, the one-letter code should be given as 'X'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. ; _item.name '_chem_comp.one_letter_code' _item.category_id chem_comp _item.mandatory_code no _item_type.code uchar1 loop_ _item_examples.case _item_examples.detail A 'alanine or adenine' B 'ambiguous asparagine/aspartic acid' R 'arginine' N 'asparagine' D 'aspartic acid' C 'cysteine or cystine or cytosine' Q 'glutamine' E 'glutamic acid' Z 'ambiguous glutamine/glutamic acid' G 'glycine or guanine' H 'histidine' I 'isoleucine' L 'leucine' K 'lysine' M 'methionine' F 'phenylalanine' P 'proline' S 'serine' T 'threonine or thymine' W 'tryptophan' Y 'tyrosine' V 'valine' U 'uracil' O 'water' X 'other' save_ save__chem_comp.three_letter_code _item_description.description ; For standard polymer components, the three-letter code for the component. If there is not a standard three-letter code for this component, or if this is a non-polymer component, the three-letter code should be given as 'UNK'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. ; _item.name '_chem_comp.three_letter_code' _item.category_id chem_comp _item.mandatory_code no _item_type.code uchar3 loop_ _item_examples.case _item_examples.detail ALA 'alanine' ARG 'arginine' ASN 'asparagine' ASP 'aspartic acid' ASX 'ambiguous asparagine/aspartic acid' CYS 'cysteine' GLN 'glutamine' GLU 'glutamic acid' GLY 'glycine' GLX 'ambiguous glutamine/glutamic acid' HIS 'histidine' ILE 'isoleucine' LEU 'leucine' LYS 'lysine' MET 'methionine' PHE 'phenylalanine' PRO 'proline' SER 'serine' THR 'threonine' TRP 'tryptophan' TRY 'tyrosine' VAL 'valine' 1MA '1-methyladenosine' 5MC '5-methylcytosine' OMC '2(prime)-O-methylcytodine' 1MG '1-methylguanosine' 2MG 'N(2)-methylguanosine' M2G 'N(2)-dimethylguanosine' 7MG '7-methylguanosine' 0MG '2(prime)-O-methylguanosine' H2U 'dihydrouridine' 5MU 'ribosylthymidine' PSU 'pseudouridine' ACE 'acetic acid' FOR 'formic acid' HOH 'water' UNK 'other' save_ save__chem_comp.type _item_description.description ; For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.type' chem_comp yes '_chem_comp_link.type_comp_1' chem_comp_link yes '_chem_comp_link.type_comp_2' chem_comp_link yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_link.type_comp_1' '_chem_comp.type' '_chem_comp_link.type_comp_2' '_chem_comp.type' _item_type.code uline loop_ _item_enumeration.value 'D-peptide linking' 'L-peptide linking' 'D-peptide NH3 amino terminus' 'L-peptide NH3 amino terminus' 'D-peptide COOH carboxy terminus' 'L-peptide COOH carboxy terminus' 'DNA linking' 'RNA linking' 'DNA OH 5 prime terminus' 'RNA OH 5 prime terminus' 'DNA OH 3 prime terminus' 'RNA OH 3 prime terminus' 'D-saccharide 1,4 and 1,4 linking' 'L-saccharide 1,4 and 1,4 linking' 'D-saccharide 1,4 and 1,6 linking' 'L-saccharide 1,4 and 1,6 linking' 'L-saccharide' 'D-saccharide' 'saccharide' 'non-polymer' 'other' save_ ##################### ## CHEM_COMP_ANGLE ## ##################### save_chem_comp_angle _category.description ; Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. ; _category.id chem_comp_angle _category.mandatory_code no loop_ _category_key.name '_chem_comp_angle.comp_id' '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_2' '_chem_comp_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_dist phe N CA C xxx.xx x.xx phe CA C O xxx.xx x.xx phe CB CA C xxx.xx x.xx phe CB CA N xxx.xx x.xx phe CA CB CG xxx.xx x.xx phe CB CG CD1 xxx.xx x.xx phe CB CG CD2 xxx.xx x.xx phe CD1 CG CD2 xxx.xx x.xx phe CG CD1 CE1 xxx.xx x.xx phe CD1 CE1 CZ xxx.xx x.xx phe CE1 CZ CE2 xxx.xx x.xx phe CZ CE2 CD2 xxx.xx x.xx phe CG CD2 CE2 xxx.xx x.xx val N CA C xxx.xx x.xx val CA C O xxx.xx x.xx val CB CA C xxx.xx x.xx val CB CA N xxx.xx x.xx val CA CB CG1 xxx.xx x.xx val CA CB CG2 xxx.xx x.xx val CG1 CB CG2 xxx.xx x.xx ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_angle.atom_id_1 _item_description.description ; The ID of the first of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_angle.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_2' '_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_2 _item_description.description ; The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_angle.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_3 _item_description.description ; The ID of the third of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_angle.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_2' save_ save__chem_comp_angle.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_angle.comp_id' _item.mandatory_code yes save_ save__chem_comp_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_comp_angle.value_angle' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_comp_angle.value_angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_angle. ; _item.name '_chem_comp_angle.value_angle_esd' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_comp_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_comp_angle.value_dist' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_angle.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_dist. ; _item.name '_chem_comp_angle.value_dist_esd' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_ATOM ## #################### save_chem_comp_atom _category.description ; Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories. ; _category.id chem_comp_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_atom.comp_id' '_chem_comp_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.substruct_code _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z phe N N main 1.20134 0.84658 0.00000 phe CA C main 0.00000 0.00000 0.00000 phe C C main -1.25029 0.88107 0.00000 phe O O main -2.18525 0.66029 -0.78409 phe CB C side 0.00662 -1.03603 1.11081 phe CG C side 0.03254 -0.49711 2.50951 phe CD1 C side -1.15813 -0.12084 3.13467 phe CE1 C side -1.15720 0.38038 4.42732 phe CZ C side 0.05385 0.51332 5.11032 phe CE2 C side 1.26137 0.11613 4.50975 phe CD2 C side 1.23668 -0.38351 3.20288 val N N main 1.20134 0.84658 0.00000 val CA C main 0.00000 0.00000 0.00000 val C C main -1.25029 0.88107 0.00000 val O O main -2.18525 0.66029 -0.78409 val CB C side 0.05260 -0.99339 1.17429 val CG1 C side -0.13288 -0.31545 2.52668 val CG2 C side -0.94265 -2.12930 0.99811 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_atom.alt_atom_id _item_description.description ; An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. ; _item.name '_chem_comp_atom.alt_atom_id' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code line save_ save__chem_comp_atom.atom_id _item_description.description ; The value of _chem_comp_atom.atom_id must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_atom.atom_id' chem_comp_atom yes '_atom_site.label_atom_id' atom_site no '_chem_comp_angle.atom_id_1' chem_comp_angle yes '_chem_comp_angle.atom_id_2' chem_comp_angle yes '_chem_comp_angle.atom_id_3' chem_comp_angle yes '_chem_comp_bond.atom_id_1' chem_comp_bond yes '_chem_comp_bond.atom_id_2' chem_comp_bond yes '_chem_comp_chir.atom_id' chem_comp_chir yes '_chem_comp_chir_atom.atom_id' chem_comp_chir_atom yes '_chem_comp_plane_atom.atom_id' chem_comp_plane_atom yes '_chem_comp_tor.atom_id_1' chem_comp_tor yes '_chem_comp_tor.atom_id_2' chem_comp_tor yes '_chem_comp_tor.atom_id_3' chem_comp_tor yes '_chem_comp_tor.atom_id_4' chem_comp_tor yes '_geom_angle.atom_site_label_atom_id_1' geom_angle no '_geom_angle.atom_site_label_atom_id_2' geom_angle no '_geom_angle.atom_site_label_atom_id_3' geom_angle no '_geom_bond.atom_site_label_atom_id_1' geom_bond no '_geom_bond.atom_site_label_atom_id_2' geom_bond no '_geom_contact.atom_site_label_atom_id_1' geom_contact no '_geom_contact.atom_site_label_atom_id_2' geom_contact no '_geom_hbond.atom_site_label_atom_id_A' geom_hbond no '_geom_hbond.atom_site_label_atom_id_D' geom_hbond no '_geom_hbond.atom_site_label_atom_id_H' geom_hbond no '_geom_torsion.atom_site_label_atom_id_1' geom_torsion no '_geom_torsion.atom_site_label_atom_id_2' geom_torsion no '_geom_torsion.atom_site_label_atom_id_3' geom_torsion no '_geom_torsion.atom_site_label_atom_id_4' geom_torsion no '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_sheet_hbond.range_1_beg_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_1_end_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_beg_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_end_label_atom_id' struct_sheet_hbond yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_3' '_chem_comp_atom.atom_id' '_chem_comp_bond.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_bond.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_chir.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_chir_atom.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_plane_atom.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_3' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_4' '_chem_comp_atom.atom_id' '_geom_angle.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_angle.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_angle.atom_site_label_atom_id_3' '_atom_site.label_atom_id' '_geom_bond.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_bond.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_contact.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_contact.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_A' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_D' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_H' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_3' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_4' '_atom_site.label_atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_1_beg_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_1_end_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_2_beg_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_2_end_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code atcode save_ save__chem_comp_atom.charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chem_comp_atom.charge' _item.category_id chem_comp_atom _item.mandatory_code no _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__chem_comp_atom.model_Cartn_x _item_description.description ; The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. ; _item.name '_chem_comp_atom.model_Cartn_x' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_y' '_chem_comp_atom.model_Cartn_z' _item_related.related_name '_chem_comp_atom.model_Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_x. ; _item.name '_chem_comp_atom.model_Cartn_x_esd' _item.category_id chem_comp_atom _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_y_esd' '_chem_comp_atom.model_Cartn_z_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_y _item_description.description ; The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. ; _item.name '_chem_comp_atom.model_Cartn_y' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x' '_chem_comp_atom.model_Cartn_z' _item_related.related_name '_chem_comp_atom.model_Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_y. ; _item.name '_chem_comp_atom.model_Cartn_y_esd' _item.category_id chem_comp_atom _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x_esd' '_chem_comp_atom.model_Cartn_z_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_z _item_description.description ; The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. ; _item.name '_chem_comp_atom.model_Cartn_z' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x' '_chem_comp_atom.model_Cartn_y' _item_related.related_name '_chem_comp_atom.model_Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_z. ; _item.name '_chem_comp_atom.model_Cartn_z_esd' _item.category_id chem_comp_atom _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x_esd' '_chem_comp_atom.model_Cartn_y_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_atom.partial_charge _item_description.description ; The partial charge assigned to this atom. ; _item.name '_chem_comp_atom.partial_charge' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code float save_ save__chem_comp_atom.substruct_code _item_description.description ; This data item assigns the atom to a substructure of the component, if appropriate. ; _item.name '_chem_comp_atom.substruct_code' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail main 'main chain of an amino acid' side 'side chain of an amino acid' base 'base of a nucleic acid' phos 'phosphate of a nucleic acid' sugar 'sugar of a nucleic acid' none 'not appropriate for this monomer' save_ #save_chem_comp_atom.type_energy # _item_description.description #; This data item is a pointer to _atom_type_energy.type in the # ATOM_TYPE_ENERGY category. #; # save_ save__chem_comp_atom.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_chem_comp_atom.type_symbol' _item.mandatory_code yes save_ #################### ## CHEM_COMP_BOND ## #################### save_chem_comp_bond _category.description ; Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. ; _category.id chem_comp_bond _category.mandatory_code no loop_ _category_key.name '_chem_comp_bond.comp_id' '_chem_comp_bond.atom_id_1' '_chem_comp_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order phe N CA sing phe CA C sing phe C O doub phe CB CA sing phe CB CG sing phe CG CD1 arom phe CD1 CE1 arom phe CE1 CZ arom phe CZ CE2 arom phe CE2 CD2 arom phe CD2 CG arom val N CA sing val CA C sing val C O doub val CB CA sing val CB CG1 sing val CB CG2 sing ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_bond.atom_id_1 _item_description.description ; The ID of the first of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_bond.atom_id_1' _item.mandatory_code yes _item_dependent.dependent_name '_chem_comp_bond.atom_id_2' save_ save__chem_comp_bond.atom_id_2 _item_description.description ; The ID of the second of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_bond.atom_id_2' _item.mandatory_code yes _item_dependent.dependent_name '_chem_comp_bond.atom_id_1' save_ save__chem_comp_bond.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_bond.comp_id' _item.mandatory_code yes save_ save__chem_comp_bond.value_order _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_chem_comp_bond.value_order' _item.category_id chem_comp_bond _item.mandatory_code no _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' save_ save__chem_comp_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_chem_comp_bond.value_dist' _item.category_id chem_comp_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_bond.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_bond.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_bond.value_dist. ; _item.name '_chem_comp_bond.value_dist_esd' _item.category_id chem_comp_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_bond.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_CHIR ## #################### save_chem_comp_chir _category.description ; Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. ; _category.id chem_comp_chir _category.mandatory_code no loop_ _category_key.name '_chem_comp_chir.comp_id' '_chem_comp_chir.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id phe phe1 CA val val1 CA # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_chir.atom_id _item_description.description ; The ID of the atom that is a chiral centre. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_chir.atom_id' _item.mandatory_code yes save_ save__chem_comp_chir.atom_config _item_description.description ; The chiral configuration of the atom that is a chiral centre. ; _item.name '_chem_comp_chir.atom_config' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail R 'absolute configuration R' S 'absolute configuration S' save_ save__chem_comp_chir.id _item_description.description ; The value of _chem_comp_chir.id must uniquely identify a record in the CHEM_COMP_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_chir.id' chem_comp_chir yes '_chem_comp_chir_atom.chir_id' chem_comp_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_chir_atom.chir_id' '_chem_comp_chir.id' _item_type.code code save_ save__chem_comp_chir.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_chir.comp_id' _item.mandatory_code yes save_ save__chem_comp_chir.number_atoms_all _item_description.description ; The total number of atoms bonded to the atom specified by _chem_comp_chir.atom_id. ; _item.name '_chem_comp_chir.number_atoms_all' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code int save_ save__chem_comp_chir.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _chem_comp_chir.atom_id. ; _item.name '_chem_comp_chir.number_atoms_nh' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code int save_ save__chem_comp_chir.volume_flag _item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_chem_comp_chir.volume_flag' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only' save_ save__chem_comp_chir.volume_three _item_description.description ; The chiral volume, V~c~, for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product ; _item.name '_chem_comp_chir.volume_three' _item.category_id chem_comp_chir _item.mandatory_code no _item_related.related_name '_chem_comp_chir.volume_three_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__chem_comp_chir.volume_three_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_chir.volume_three. ; _item.name '_chem_comp_chir.volume_three_esd' _item.category_id chem_comp_chir _item.mandatory_code no _item_related.related_name '_chem_comp_chir.volume_three' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ ######################### ## CHEM_COMP_CHIR_ATOM ## ######################### save_chem_comp_chir_atom _category.description ; Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. ; _category.id chem_comp_chir_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_chir_atom.chir_id' '_chem_comp_chir_atom.atom_id' '_chem_comp_chir_atom.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_chir_atom.comp_id _chem_comp_chir_atom.chir_id _chem_comp_chir_atom.atom_id phe 1 N phe 1 C phe 1 CB val 1 N val 1 C val 1 CB # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_chir_atom.atom_id _item_description.description ; The ID of an atom bonded to the chiral atom. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_chir_atom.atom_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.chir_id _item_description.description ; This data item is a pointer to _chem_comp_chir.id in the CHEM_COMP_CHIR category. ; _item.name '_chem_comp_chir_atom.chir_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_chir_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.dev _item_description.description ; The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_chem_comp_chir_atom.dev' _item.category_id chem_comp_chir_atom _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_LINK ## #################### save_chem_comp_link _category.description ; Data items in the CHEM_COMP_LINK category give details about the links between chemical components. ; _category.id chem_comp_link _category.mandatory_code no _category_key.name '_chem_comp_link.link_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' # loop_ # _category_examples.detail # _category_examples.case # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ; # Example 1 - from nucleotide external reference dictionary Nucleic # Database Project 1997. # ; # ; # _chem_comp_link.link_id ribose_adenine # _chem_comp_link.type_comp_1 ribose # _chem_comp_link.type_comp_2 adenine # _chem_comp_link.details # ; # Defines the linkage between adenine base and ribose sugar # ; # ; # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_link.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_comp_link.link_id' _item.mandatory_code yes save_ save__chem_comp_link.details _item_description.description ; A description of special aspects of a link between chemical components in the structure. ; _item.name '_chem_comp_link.details' _item.category_id chem_comp_link _item.mandatory_code no _item_type.code text save_ save__chem_comp_link.type_comp_1 _item_description.description ; The type of the first of the two components joined by the link. This data item is a pointer to _chem_comp.type in the CHEM_COMP category. ; _item.name '_chem_comp_link.type_comp_1' _item.mandatory_code yes save_ save__chem_comp_link.type_comp_2 _item_description.description ; The type of the second of the two components joined by the link. This data item is a pointer to _chem_comp.type in the CHEM_COMP category. ; _item.name '_chem_comp_link.type_comp_2' _item.mandatory_code yes save_ ##################### ## CHEM_COMP_PLANE ## ##################### save_chem_comp_plane _category.description ; Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. ; _category.id chem_comp_plane _category.mandatory_code no loop_ _category_key.name '_chem_comp_plane.comp_id' '_chem_comp_plane.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_plane.comp_id _chem_comp_plane.id phe phe1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_plane.id _item_description.description ; The value of _chem_comp_plane.id must uniquely identify a record in the CHEM_COMP_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_plane.id' chem_comp_plane yes '_chem_comp_plane_atom.plane_id' chem_comp_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_plane_atom.plane_id' '_chem_comp_plane.id' _item_type.code code save_ save__chem_comp_plane.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_plane.comp_id' _item.mandatory_code yes save_ save__chem_comp_plane.number_atoms_all _item_description.description ; The total number of atoms in the plane. ; _item.name '_chem_comp_plane.number_atoms_all' _item.category_id chem_comp_plane _item.mandatory_code no _item_type.code int save_ save__chem_comp_plane.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_chem_comp_plane.number_atoms_nh' _item.category_id chem_comp_plane _item.mandatory_code no _item_type.code int save_ ########################## ## CHEM_COMP_PLANE_ATOM ## ########################## save_chem_comp_plane_atom _category.description ; Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. ; _category.id chem_comp_plane_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_plane_atom.plane_id' '_chem_comp_plane_atom.atom_id' '_chem_comp_plane_atom.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.atom_id phe1 phe CB phe1 phe CG phe1 phe CD1 phe1 phe CE1 phe1 phe CZ phe1 phe CE2 phe1 phe CD2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_plane_atom.atom_id _item_description.description ; The ID of an atom involved in the plane. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_plane_atom.atom_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_plane_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.plane_id _item_description.description ; This data item is a pointer to _chem_comp_plane.id in the CHEM_COMP_PLANE category. ; _item.name '_chem_comp_plane_atom.plane_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.dist_esd _item_description.description ; This data item is the standard deviation of the out-of-plane distance for this atom. ; _item.name '_chem_comp_plane_atom.dist_esd' _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_TOR ## #################### save_chem_comp_tor _category.description ; Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. ; _category.id chem_comp_tor _category.mandatory_code no loop_ _category_key.name '_chem_comp_tor.comp_id' '_chem_comp_tor.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 phe phe_chi1 N CA CB CG phe phe_chi2 CA CB CG CD1 phe phe_ring1 CB CG CD1 CE1 phe phe_ring2 CB CG CD2 CE2 phe phe_ring3 CG CD1 CE1 CZ phe phe_ring4 CD1 CE1 CZ CE2 phe phe_ring5 CE1 CZ CE2 CD2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_tor.atom_id_1 _item_description.description ; The ID of the first of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_3' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_2 _item_description.description ; The ID of the second of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_3' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_3 _item_description.description ; The ID of the third of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_4 _item_description.description ; The ID of the fourth of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_4' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_3' save_ save__chem_comp_tor.id _item_description.description ; The value of _chem_comp_tor.id must uniquely identify a record in the CHEM_COMP_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_tor.id' chem_comp_tor yes '_chem_comp_tor_value.tor_id' chem_comp_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_tor_value.tor_id' '_chem_comp_tor.id' _item_type.code code save_ save__chem_comp_tor.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_tor.comp_id' _item.mandatory_code yes save_ ########################## ## CHEM_COMP_TOR_VALUE ## ########################## save_chem_comp_tor_value _category.description ; Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id chem_comp_tor_value _category.mandatory_code no loop_ _category_key.name '_chem_comp_tor_value.tor_id' '_chem_comp_tor_value.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _chem_comp_tor_value.tor_id _chem_comp_tor_value.comp_id _chem_comp_tor_value.angle _chem_comp_tor_value.dist phe_chi1 phe -60.0 2.88 phe_chi1 phe 180.0 3.72 phe_chi1 phe 60.0 2.88 phe_chi2 phe 90.0 3.34 phe_chi2 phe -90.0 3.34 phe_ring1 phe 180.0 3.75 phe_ring2 phe 180.0 3.75 phe_ring3 phe 0.0 2.80 phe_ring4 phe 0.0 2.80 phe_ring5 phe 0.0 2.80 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_tor_value.comp_id _item_description.description ; This data item is a pointer to _chem_comp_atom.comp_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor_value.comp_id' _item.mandatory_code yes save_ save__chem_comp_tor_value.tor_id _item_description.description ; This data item is a pointer to _chem_comp_tor.id in the CHEM_COMP_TOR category. ; _item.name '_chem_comp_tor_value.tor_id' _item.mandatory_code yes save_ save__chem_comp_tor_value.angle _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_comp_tor_value.angle' _item.category_id chem_comp_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_comp_tor_value.angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_comp_tor_value.angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_tor_value.angle. ; _item.name '_chem_comp_tor_value.angle_esd' _item.category_id chem_comp_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_comp_tor_value.angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_comp_tor_value.dist _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_chem_comp_tor_value.dist' _item.category_id chem_comp_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_tor_value.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_tor_value.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_tor_value.dist. ; _item.name '_chem_comp_tor_value.dist_esd' _item.category_id chem_comp_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_tor_value.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ############### ## CHEM_LINK ## ############### save_chem_link _category.description ; Data items in the CHEM_LINK category give details about the links between chemical components. ; _category.id chem_link _category.mandatory_code no _category_key.name '_chem_link.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link.id _item_description.description ; The value of _chem_link.id must uniquely identify each item in the CHEM_LINK list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link.id' chem_link yes '_chem_link_angle.link_id' chem_link_angle yes '_chem_link_bond.link_id' chem_link_bond yes '_chem_link_chir.link_id' chem_link_chir yes '_chem_link_plane.link_id' chem_link_plane yes '_chem_link_tor.link_id' chem_link_tor yes '_chem_comp_link.link_id' chem_comp_link yes '_entity_link.link_id' entity_link yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_angle.link_id' '_chem_link.id' '_chem_link_bond.link_id' '_chem_link.id' '_chem_link_chir.link_id' '_chem_link.id' '_chem_link_plane.link_id' '_chem_link.id' '_chem_link_tor.link_id' '_chem_link.id' '_chem_comp_link.link_id' '_chem_link.id' '_entity_link.link_id' '_chem_link.id' _item_type.code code loop_ _item_examples.case 'peptide' 'oligosaccharide 1,4' 'DNA' save_ save__chem_link.details _item_description.description ; A description of special aspects of a link between chemical components in the structure. ; _item.name '_chem_link.details' _item.category_id chem_link _item.mandatory_code no _item_type.code text save_ ##################### ## CHEM_LINK_ANGLE ## ##################### save_chem_link_angle _category.description ; Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components. ; _category.id chem_link_angle _category.mandatory_code no loop_ _category_key.name '_chem_link_angle.link_id' '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_2' '_chem_link_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. ; ; loop_ _chem_link_angle.link_id _chem_link_angle.value_angle _chem_link_angle.value_angle_esd _chem_link_angle.atom_id_1 _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.atom_3_comp_id PEPTIDE 111.2 2.8 N 1 CA 1 C 1 PEPTIDE 120.8 1.7 CA 1 C 1 O 1 PEPTIDE 116.2 2.0 CA 1 C 1 N 2 PEPTIDE 123.0 1.6 O 1 C 1 N 2 PEPTIDE 121.7 1.8 C 1 N 2 CA 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_angle.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_angle.atom_1_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_2_comp_id' '_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_angle.atom_2_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_1_comp_id' '_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_angle.atom_3_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_1_comp_id' '_chem_link_angle.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_id_1 _item_description.description ; The ID of the first of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_1_comp_id). ; _item.name '_chem_link_angle.atom_id_1' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_2' '_chem_link_angle.atom_id_3' _item_type.code code save_ save__chem_link_angle.atom_id_2 _item_description.description ; The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_2_comp_id). ; _item.name '_chem_link_angle.atom_id_2' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_3' _item_type.code code save_ save__chem_link_angle.atom_id_3 _item_description.description ; The ID of the third of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_3_comp_id). ; _item.name '_chem_link_angle.atom_id_3' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_2' _item_type.code code save_ save__chem_link_angle.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_angle.link_id' _item.mandatory_code yes save_ save__chem_link_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_link_angle.value_angle' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_angle.value_angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_angle.value_angle. ; _item.name '_chem_link_angle.value_angle_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_link_angle.value_dist' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_angle.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_dist. ; _item.name '_chem_link_angle.value_dist_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_LINK_BOND ## #################### save_chem_link_bond _category.description ; Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure. ; _category.id chem_link_bond _category.mandatory_code no loop_ _category_key.name '_chem_link_bond.link_id' '_chem_link_bond.atom_id_1' '_chem_link_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. ; ; loop_ _chem_link_bond.link_id _chem_link_bond.value_dist _chem_link_bond.value_dist_esd _chem_link_bond.atom_id_1 _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.atom_2_comp_id PEPTIDE 1.458 0.019 N 1 CA 1 PEPTIDE 1.525 0.021 CA 1 C 1 PEPTIDE 1.329 0.014 C 1 N 2 PEPTIDE 1.231 0.020 C 1 O 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_bond.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_bond.atom_1_comp_id' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_bond.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_bond.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link. ; _item.name '_chem_link_bond.atom_2_comp_id' _item.category_id chem_link_bond _item.mandatory_code no _item_dependent.dependent_name '_chem_link_bond.atom_1_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_bond.atom_id_1 _item_description.description ; The ID of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_bond.atom_id_1' _item.category_id chem_link_bond _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_bond.atom_id_2' _item_type.code code save_ save__chem_link_bond.atom_id_2 _item_description.description ; The ID of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_chem_link_bond.atom_id_2' _item.category_id chem_link_bond _item.mandatory_code yes _item_dependent.dependent_name '_chem_link_bond.atom_id_1' _item_type.code code save_ save__chem_link_bond.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_bond.link_id' _item.mandatory_code yes save_ save__chem_link_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_chem_link_bond.value_dist' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_bond.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_bond.value_dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_bond.value_dist. ; _item.name '_chem_link_bond.value_dist_esd' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_bond.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__chem_link_bond.value_order _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_chem_link_bond.value_order' _item.category_id chem_link_bond _item.mandatory_code no _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' save_ #################### ## CHEM_LINK_CHIR ## #################### save_chem_link_chir _category.description ; Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. ; _category.id chem_link_chir _category.mandatory_code no loop_ _category_key.name '_chem_link_chir.link_id' '_chem_link_chir.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_chir.atom_comp_id _item_description.description ; This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_chir.atom_comp_id' _item.category_id chem_link_chir _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_chir.atom_id _item_description.description ; The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_chir.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_chir.atom_config _item_description.description ; The chiral configuration of the atom that is a chiral centre. ; _item.name '_chem_link_chir.atom_config' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail R 'absolute configuration R' S 'absolute configuration S' save_ save__chem_link_chir.id _item_description.description ; The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_chir.id' chem_link_chir yes '_chem_link_chir_atom.chir_id' chem_link_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_chir_atom.chir_id' '_chem_link_chir.id' _item_type.code code save_ save__chem_link_chir.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_chir.link_id' _item.mandatory_code yes save_ save__chem_link_chir.number_atoms_all _item_description.description ; The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id. ; _item.name '_chem_link_chir.number_atoms_all' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code int save_ save__chem_link_chir.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id. ; _item.name '_chem_link_chir.number_atoms_nh' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code int save_ save__chem_link_chir.volume_flag _item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_chem_link_chir.volume_flag' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only' save_ save__chem_link_chir.volume_three _item_description.description ; The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_link_chir.atom_id to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_link_chir.atom_id to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_link_chir.atom_id to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product ; _item.name '_chem_link_chir.volume_three' _item.category_id chem_link_chir _item.mandatory_code no _item_related.related_name '_chem_link_chir.volume_three_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__chem_link_chir.volume_three_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_chir.volume_three. ; _item.name '_chem_link_chir.volume_three_esd' _item.category_id chem_link_chir _item.mandatory_code no _item_related.related_name '_chem_link_chir.volume_three' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ ######################### ## CHEM_LINK_CHIR_ATOM ## ######################### save_chem_link_chir_atom _category.description ; Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components. ; _category.id chem_link_chir_atom _category.mandatory_code no loop_ _category_key.name '_chem_link_chir_atom.chir_id' '_chem_link_chir_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_chir_atom.atom_comp_id _item_description.description ; This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_chir_atom.atom_comp_id' _item.category_id chem_link_chir_atom _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_chir_atom.atom_id _item_description.description ; The ID of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_chir_atom.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_chir_atom.chir_id _item_description.description ; This data item is a pointer to _chem_link_chir.id in the CHEM_LINK_CHIR category. ; _item.name '_chem_link_chir_atom.chir_id' _item.mandatory_code yes save_ save__chem_link_chir_atom.dev _item_description.description ; The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_chem_link_chir_atom.dev' _item.category_id chem_link_chir_atom _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ ##################### ## CHEM_LINK_PLANE ## ##################### save_chem_link_plane _category.description ; Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. ; _category.id chem_link_plane _category.mandatory_code no loop_ _category_key.name '_chem_link_plane.link_id' '_chem_link_plane.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_plane.id _item_description.description ; The value of _chem_link_plane.id must uniquely identify a record in the CHEM_LINK_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_plane.id' chem_link_plane yes '_chem_link_plane_atom.plane_id' chem_link_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_plane_atom.plane_id' '_chem_link_plane.id' _item_type.code code save_ save__chem_link_plane.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_plane.link_id' _item.mandatory_code yes save_ save__chem_link_plane.number_atoms_all _item_description.description ; The total number of atoms in the plane. ; _item.name '_chem_link_plane.number_atoms_all' _item.category_id chem_link_plane _item.mandatory_code no _item_type.code int save_ save__chem_link_plane.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_chem_link_plane.number_atoms_nh' _item.category_id chem_link_plane _item.mandatory_code no _item_type.code int save_ ########################## ## CHEM_LINK_PLANE_ATOM ## ########################## save_chem_link_plane_atom _category.description ; Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components. ; _category.id chem_link_plane_atom _category.mandatory_code no loop_ _category_key.name '_chem_link_plane_atom.plane_id' '_chem_link_plane_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_plane_atom.atom_comp_id _item_description.description ; This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_plane_atom.atom_comp_id' _item.category_id chem_link_plane_atom _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_plane_atom.atom_id _item_description.description ; The ID of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_plane_atom.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_plane_atom.plane_id _item_description.description ; This data item is a pointer to _chem_link_plane.id in the CHEM_LINK_PLANE category. ; _item.name '_chem_link_plane_atom.plane_id' _item.mandatory_code yes save_ ################### ## CHEM_LINK_TOR ## ################### save_chem_link_tor _category.description ; Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. ; _category.id chem_link_tor _category.mandatory_code no loop_ _category_key.name '_chem_link_tor.link_id' '_chem_link_tor.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_tor.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_1_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_3_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_2_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_3_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_3_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_4_comp_id _item_description.description ; This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link. ; _item.name '_chem_link_tor.atom_4_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_id_1 _item_description.description ; The ID of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_3' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_2 _item_description.description ; The ID of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_3' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_3 _item_description.description ; The ID of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_4 _item_description.description ; The ID of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_4' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_3' _item_type.code code save_ save__chem_link_tor.id _item_description.description ; The value of _chem_link_tor.id must uniquely identify a record in the CHEM_LINK_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_tor.id' chem_link_tor yes '_chem_link_tor_value.tor_id' chem_link_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_tor_value.tor_id' '_chem_link_tor.id' _item_type.code code save_ save__chem_link_tor.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_tor.link_id' _item.mandatory_code yes save_ ######################### ## CHEM_LINK_TOR_VALUE ## ######################### save_chem_link_tor_value _category.description ; Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id chem_link_tor_value _category.mandatory_code no _category_key.name '_chem_link_tor_value.tor_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__chem_link_tor_value.tor_id _item_description.description ; This data item is a pointer to _chem_link_tor.id in the CHEM_LINK_TOR category. ; _item.name '_chem_link_tor_value.tor_id' _item.mandatory_code yes save_ save__chem_link_tor_value.angle _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_link_tor_value.angle' _item.category_id chem_link_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_link_tor_value.angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_tor_value.angle_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_tor_value.angle. ; _item.name '_chem_link_tor_value.angle_esd' _item.category_id chem_link_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_link_tor_value.angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_tor_value.dist _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_chem_link_tor_value.dist' _item.category_id chem_link_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_tor_value.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_tor_value.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _chem_link_tor_value.dist. ; _item.name '_chem_link_tor_value.dist_esd' _item.category_id chem_link_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_tor_value.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ############## ## CHEMICAL ## ############## save_chemical _category.description ; Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. ; _category.id chemical _category.mandatory_code no _category_key.name '_chemical.entry_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. ; ; _chemical.entry_id '9597gaus' _chemical.name_systematic trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0) ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_chemical.entry_id' _item.mandatory_code yes save_ save__chemical.compound_source _item_description.description ; Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. ; _item.name '_chemical.compound_source' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_compound_source' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'From Norilsk (USSR)' 'Extracted from the bark of Cinchona Naturalis' save_ save__chemical.melting_point _item_description.description ; The temperature in kelvins at which the crystalline solid changes to a liquid. ; _item.name '_chemical.melting_point' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_melting_point' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code kelvins save_ save__chemical.name_common _item_description.description ; Trivial name by which the compound is commonly known. ; _item.name '_chemical.name_common' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_common' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '1-bromoestradiol' save_ save__chemical.name_mineral _item_description.description ; Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical.compound_source. ; _item.name '_chemical.name_mineral' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_mineral' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'chalcopyrite' save_ save__chemical.name_structure_type _item_description.description ; Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. ; _item.name '_chemical.name_structure_type' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_structure_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'perovskite' 'sphalerite' 'A15' save_ save__chemical.name_systematic _item_description.description ; IUPAC or Chemical Abstracts full name of the compound. ; _item.name '_chemical.name_systematic' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_systematic' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '1-bromoestra-1,3,5(10)-triene-3,17\b-diol' save_ ######################## ## CHEMICAL_CONN_ATOM ## ######################## save_chemical_conn_atom _category.description ; Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. ; _category.id chemical_conn_atom _category.mandatory_code no _category_key.name '_chemical_conn_atom.number' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; ; loop_ _chemical_conn_atom.number _chemical_conn_atom.type_symbol _chemical_conn_atom.display_x _chemical_conn_atom.display_y _chemical_conn_atom.NCA _chemical_conn_atom.NH 1 S .39 .81 1 0 2 S .39 .96 2 0 3 N .14 .88 3 0 4 C .33 .88 3 0 5 C .11 .96 2 2 6 C .03 .96 2 2 7 C .03 .80 2 2 8 C .11 .80 2 2 9 S .54 .81 1 0 10 S .54 .96 2 0 11 N .80 .88 3 0 12 C .60 .88 3 0 13 C .84 .96 2 2 14 C .91 .96 2 2 15 C .91 .80 2 2 16 C .84 .80 2 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_conn_atom.charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chemical_conn_atom.charge' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_charge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__chemical_conn_atom.display_x _item_description.description ; The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. ; _item.name '_chemical_conn_atom.display_x' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_atom.display_y' loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__chemical_conn_atom.display_y _item_description.description ; The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. ; _item.name '_chemical_conn_atom.display_y' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_atom.display_x' loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__chemical_conn_atom.NCA _item_description.description ; The number of connected atoms excluding terminal hydrogen atoms. ; _item.name '_chemical_conn_atom.NCA' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NCA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__chemical_conn_atom.NH _item_description.description ; The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the ATOM_SITE list. ; _item.name '_chemical_conn_atom.NH' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NH' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__chemical_conn_atom.number _item_description.description ; The chemical sequence number to be associated with this atom. Within an ATOM_SITE list, this number must match one of the _atom_site.chemical_conn_number values. ; loop_ _item.name _item.category_id _item.mandatory_code '_chemical_conn_atom.number' chemical_conn_atom yes '_atom_site.chemical_conn_number' atom_site no '_chemical_conn_bond.atom_1' chemical_conn_bond yes '_chemical_conn_bond.atom_2' chemical_conn_bond yes _item_aliases.alias_name '_chemical_conn_atom_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.chemical_conn_number' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_1' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_2' '_chemical_conn_atom.number' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chemical_conn_atom.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_chemical_conn_atom.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_atom_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ ######################## ## CHEMICAL_CONN_BOND ## ######################## save_chemical_conn_bond _category.description ; Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms. ; _category.id chemical_conn_bond _category.mandatory_code no loop_ _category_key.name '_chemical_conn_bond.atom_1' '_chemical_conn_bond.atom_2' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. ; ; loop_ _chemical_conn_bond.atom_1 _chemical_conn_bond.atom_2 _chemical_conn_bond.type 4 1 doub 4 3 sing 4 2 sing 5 3 sing 6 5 sing 7 6 sing 8 7 sing 8 3 sing 10 2 sing 12 9 doub 12 11 sing 12 10 sing 13 11 sing 14 13 sing 15 14 sing 16 15 sing 16 11 sing 17 5 sing 18 5 sing 19 6 sing 20 6 sing 21 7 sing 22 7 sing 23 8 sing 24 8 sing 25 13 sing 26 13 sing 27 14 sing 28 14 sing 29 15 sing 30 15 sing 31 16 sing 32 16 sing ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_conn_bond.atom_1 _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_chemical_conn_bond.atom_1' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_bond_atom_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_bond.atom_2' save_ save__chemical_conn_bond.atom_2 _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_chemical_conn_bond.atom_2' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_bond_atom_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_chemical_conn_bond.atom_1' save_ save__chemical_conn_bond.type _item_description.description ; The chemical bond type associated with the connection between the two sites _chemical_conn_bond.atom_1 and _chemical_conn_bond.atom_2. ; _item.name '_chemical_conn_bond.type' _item.category_id chemical_conn_bond _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_bond_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalized double bond' pi 'pi bond' save_ ###################### ## CHEMICAL_FORMULA ## ###################### save_chemical_formula _category.description ; Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. ; _category.id chemical_formula _category.mandatory_code no _category_key.name '_chemical_formula.entry_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _chemical_formula.entry_id 'TOZ' _chemical_formula.moiety 'C18 H25 N O3' _chemical_formula.sum 'C18 H25 N O3' _chemical_formula.weight 303.40 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_formula.analytical _item_description.description ; Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (estimated standard deviations). ; _item.name '_chemical_formula.analytical' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_analytical' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Fe2.45(2) Ni1.60(3) S4' save_ save__chemical_formula.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_chemical_formula.entry_id' _item.mandatory_code yes save_ save__chemical_formula.iupac _item_description.description ; Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. ; _item.name '_chemical_formula.iupac' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_iupac' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' save_ save__chemical_formula.moiety _item_description.description ; Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the CHEMICAL_FORMULA category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. ; _item.name '_chemical_formula.moiety' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_moiety' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'C7 H4 Cl Hg N O3 S' 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-' 'C12 H16 N2 O6, 5(H2 O1)' "(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)" save_ save__chemical_formula.structural _item_description.description ; See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site data should not be included in this formula (see also _chemical_formula.analytical). ; _item.name '_chemical_formula.structural' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_structural' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Ca ((Cl O3)2 O)2 (H2 O)6' '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' save_ save__chemical_formula.sum _item_description.description ; See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the CHEMICAL_FORMULA category description. Parentheses are not normally used. ; _item.name '_chemical_formula.sum' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_sum' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chemical_formula.weight _item_description.description ; Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal.density_diffrn. ; _item.name '_chemical_formula.weight' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chemical_formula.weight_meas _item_description.description ; Formula mass in daltons measured by a non-diffraction experiment. ; _item.name '_chemical_formula.weight_meas' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ ############## ## CITATION ## ############## save_citation _category.description ; Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. ; _category.id citation _category.mandatory_code no _category_key.name '_citation.id' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _citation.id _citation.coordinate_linkage _citation.title _citation.country _citation.journal_abbrev _citation.journal_volume _citation.journal_issue _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_title _citation.book_publisher _citation.book_id_ISBN _citation.details primary yes ; Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution. ; US 'J. Biol. Chem.' 265 . 14209 14219 1990 HBCHA3 0021-9258 071 . . . ; The publication that directly relates to this coordinate set. ; 2 no ; Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1. ; UK 'Nature' 337 . 615 619 1989 NATUAS 0028-0836 006 . . . ; Determination of the structure of the unliganded enzyme. ; 3 no ; Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1. ; US 'J. Biol. Chem.' 264 . 1919 1921 1989 HBCHA3 0021-9258 071 . . . ; Crystallization of the unliganded enzyme. ; 4 no ; Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease. ; US 'J. Biol. Chem.' 264 . 2307 2312 1989 HBCHA3 0021-9258 071 . . . ; Expression and purification of the enzyme. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation.abstract _item_description.description ; Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. ; _item.name '_citation.abstract' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_abstract' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__citation.abstract_id_CAS _item_description.description ; The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. ; _item.name '_citation.abstract_id_CAS' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_abstract_id_CAS' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__citation.book_id_ISBN _item_description.description ; The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. ; _item.name '_citation.book_id_ISBN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_id_ISBN' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.book_publisher _item_description.description ; The name of the publisher of the citation; relevant for books or book chapters. ; _item.name '_citation.book_publisher' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'John Wiley and Sons' save_ save__citation.book_publisher_city _item_description.description ; The location of the publisher of the citation; relevant for books or book chapters. ; _item.name '_citation.book_publisher_city' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher_city' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'London' save_ save__citation.book_title _item_description.description ; The title of the book in which the citation appeared; relevant for books or book chapters. ; _item.name '_citation.book_title' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__citation.coordinate_linkage _item_description.description ; _citation.coordinate_linkage states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. ; _item.name '_citation.coordinate_linkage' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_coordinate_linkage' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'citation unrelated to current coordinates' n 'abbreviation for "no"' yes 'citation related to current coordinates' y 'abbreviation for "yes"' save_ save__citation.country _item_description.description ; The country of publication; relevant for books and book chapters. ; _item.name '_citation.country' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_country' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.database_id_Medline _item_description.description ; Accession number used by Medline to categorize a specific bibliographic entry. ; _item.name '_citation.database_id_Medline' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_database_id_Medline' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int _item_examples.case 89064067 save_ save__citation.details _item_description.description ; A description of special aspects of the relationship of the contents of the data block to the literature item cited. ; _item.name '_citation.details' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case ; citation relates to this precise coordinate set ; ; citation relates to earlier low-resolution structure ; ; citation relates to further refinement of structure reported in citation 2 ; save_ save__citation.id _item_description.description ; The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_citation.id' citation yes '_citation_author.citation_id' citation_author yes '_citation_editor.citation_id' citation_editor yes '_software.citation_id' software no _item_aliases.alias_name '_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_citation_author.citation_id' '_citation.id' '_citation_editor.citation_id' '_citation.id' '_software.citation_id' '_citation.id' _item_type.code code loop_ _item_examples.case 'primary' '1' '2' save_ save__citation.journal_abbrev _item_description.description ; Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. ; _item.name '_citation.journal_abbrev' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_abbrev' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'J. Mol. Biol.' save_ save__citation.journal_id_ASTM _item_description.description ; The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. ; _item.name '_citation.journal_id_ASTM' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.journal_id_CSD _item_description.description ; The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). ; _item.name '_citation.journal_id_CSD' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_CSD' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '0070' save_ save__citation.journal_id_ISSN _item_description.description ; The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_id_ISSN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ISSN' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.journal_full _item_description.description ; Full name of the cited journal; relevant for journal articles. ; _item.name '_citation.journal_full' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_full' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Journal of Molecular Biology' save_ save__citation.journal_issue _item_description.description ; Issue number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_issue' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_issue' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '2' save_ save__citation.journal_volume _item_description.description ; Volume number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_volume' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '174' save_ save__citation.language _item_description.description ; Language in which the cited article is written. ; _item.name '_citation.language' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_language' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'German' save_ save__citation.page_first _item_description.description ; The first page of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.page_first' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.page_last _item_description.description ; The last page of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.page_last' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_last' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.title _item_description.description ; The title of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.title' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Structure of diferric duck ovotransferrin at 2.35 \%A resolution. ; save_ save__citation.year _item_description.description ; The year of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.year' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_year' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int _item_examples.case 1984 save_ ##################### ## CITATION_AUTHOR ## ##################### save_citation_author _category.description ; Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. ; _category.id citation_author _category.mandatory_code no loop_ _category_key.name '_citation_author.citation_id' '_citation_author.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _citation_author.citation_id _citation_author.ordinal _citation_author.name primary 1 'Fitzgerald, P.M.D.' primary 2 'McKeever, B.M.' primary 3 'Van Middlesworth, J.F.' primary 4 'Springer, J.P.' primary 5 'Heimbach, J.C.' primary 6 'Leu, C.-T.' primary 7 'Herber, W.K.' primary 8 'Dixon, R.A.F.' primary 9 'Darke, P.L.' 2 1 'Navia, M.A.' 2 2 'Fitzgerald, P.M.D.' 2 3 'McKeever, B.M.' 2 4 'Leu, C.-T.' 2 5 'Heimbach, J.C.' 2 6 'Herber, W.K.' 2 7 'Sigal, I.S.' 2 8 'Darke, P.L.' 2 9 'Springer, J.P.' 3 1 'McKeever, B.M.' 3 2 'Navia, M.A.' 3 3 'Fitzgerald, P.M.D.' 3 4 'Springer, J.P.' 3 5 'Leu, C.-T.' 3 6 'Heimbach, J.C.' 3 7 'Herber, W.K.' 3 8 'Sigal, I.S.' 3 9 'Darke, P.L.' 4 1 'Darke, P.L.' 4 2 'Leu, C.-T.' 4 3 'Davis, L.J.' 4 4 'Heimbach, J.C.' 4 5 'Diehl, R.E.' 4 6 'Hill, W.S.' 4 7 'Dixon, R.A.F.' 4 8 'Sigal, I.S.' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_author.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_author.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_author_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__citation_author.name _item_description.description ; Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_author.name' _item.category_id citation_author _item.mandatory_code yes _item_aliases.alias_name '_citation_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' save_ save__citation_author.ordinal _item_description.description ; This data item defines the order of the author's name in the list of authors of a citation. ; _item.name '_citation_author.ordinal' _item.category_id citation_author _item.mandatory_code no _item_aliases.alias_name '_citation_author_ordinal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ ##################### ## CITATION_EDITOR ## ##################### save_citation_editor _category.description ; Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list. ; _category.id citation_editor _category.mandatory_code no loop_ _category_key.name '_citation_editor.citation_id' '_citation_editor.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _citation_editor.citation_id _citation_editor.name 5 'McKeever, B.M.' 5 'Navia, M.A.' 5 'Fitzgerald, P.M.D.' 5 'Springer, J.P.' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_editor.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_editor.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_editor_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__citation_editor.name _item_description.description ; Names of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_editor.name' _item.category_id citation_editor _item.mandatory_code no _item_aliases.alias_name '_citation_editor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' save_ save__citation_editor.ordinal _item_description.description ; This data item defines the order of the editor's name in the list of editors of a citation. ; _item.name '_citation_editor.ordinal' _item.category_id citation_editor _item.mandatory_code no _item_aliases.alias_name '_citation_editor_ordinal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ ############### ## COMPUTING ## ############### save_computing _category.description ; Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead. ; _category.id computing _category.mandatory_code no _category_key.name '_computing.entry_id' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. ; ; _computing.data_collection 'CAD-4 (Enraf-Nonius, 1989)' _computing.cell_refinement 'CAD-4 (Enraf-Nonius, 1989)' _computing.data_reduction 'CFEO (Solans, 1978)' _computing.structure_solution 'SHELXS86 (Sheldrick, 1990)' _computing.structure_refinement 'SHELXL93 (Sheldrick, 1993)' _computing.molecular_graphics 'ORTEPII (Johnson, 1976)' _computing.publication_material 'PARST (Nardelli, 1983)' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__computing.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_computing.entry_id' _item.mandatory_code yes save_ save__computing.cell_refinement _item_description.description ; Software used for cell refinement. Give the program or package name and a brief reference. ; _item.name '_computing.cell_refinement' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_cell_refinement' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'CAD4 (Enraf-Nonius, 1989)' save_ save__computing.data_collection _item_description.description ; Software used for data collection. Give the program or package name and a brief reference. ; _item.name '_computing.data_collection' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_data_collection' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'CAD4 (Enraf-Nonius, 1989)' save_ save__computing.data_reduction _item_description.description ; Software used for data reduction. Give the program or package name and a brief reference. ; _item.name '_computing.data_reduction' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_data_reduction' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)' save_ save__computing.molecular_graphics _item_description.description ; Software used for molecular graphics. Give the program or package name and a brief reference. ; _item.name '_computing.molecular_graphics' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_molecular_graphics' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'FRODO (Jones, 1986), ORTEP (Johnson, 1965)' save_ save__computing.publication_material _item_description.description ; Software used for generating material for publication. Give the program or package name and a brief reference. ; _item.name '_computing.publication_material' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_publication_material' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__computing.structure_refinement _item_description.description ; Software used for refinement of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_refinement' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_structure_refinement' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'SHELX85 (Sheldrick, 1985)' 'X-PLOR (Brunger, 1992)' save_ save__computing.structure_solution _item_description.description ; Software used for solution of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_solution' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_structure_solution' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'SHELX85 (Sheldrick, 1985)' save_ ############## ## DATABASE ## ############## save_database _category.description ; Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs. ; _category.id database _category.mandatory_code no _category_key.name '_database.entry_id' loop_ _category_group.id 'inclusive_group' 'compliance_group' save_ save__database.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_database.entry_id' _item.mandatory_code yes save_ #save__database.code_CAS # _item_description.description #; The code assigned by Chemical Abstracts. #; # _item.name '_database.code_CAS' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_CAS' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_CSD # _item_description.description #; The code assigned by the Cambridge Structural Database # (organic and metal-organic compounds). #; # _item.name '_database.code_CSD' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_CSD' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_ICSD # _item_description.description #; The code assigned by the Inorganic Crystal Structure Database. #; # _item.name '_database.code_ICSD' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_ICSD' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_MDF # _item_description.description #; The code assigned by the Metals Data File (metal structures). #; # _item.name '_database.code_MDF' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_MDF' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_NBS # _item_description.description #; The code assigned by the NBS (NIST) Crystal Data Database # (lattice parameters). #; # _item.name '_database.code_NBS' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_NBS' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # #save__database.code_PDF # _item_description.description #; The code assigned by the Powder Diffraction File (JCPDS/ICDD). #; # _item.name '_database.code_PDF' # _item.category_id database # _item.mandatory_code no # _item_aliases.alias_name '_database_code_PDF' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_related.related_name # _item_related.function_code '_database_2.database_id' # replacedby # '_database_2.database_code' # replacedby # _item_type.code line # save_ # save__database.journal_ASTM _item_description.description ; The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service. ; _item.name '_database.journal_ASTM' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_journal_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__database.journal_CSD _item_description.description ; The journal code used in the Cambridge Structural Database. ; _item.name '_database.journal_CSD' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_journal_CSD' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ################ ## DATABASE_2 ## ################ save_database_2 _category.description ; Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. ; _category.id database_2 _category.mandatory_code no loop_ _category_key.name '_database_2.database_id' '_database_2.database_code' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _database_2.database_id 'PDB' _database_2.database_code '5HVP' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_2.database_id _item_description.description ; An abbreviation that identifies the database. ; _item.name '_database_2.database_id' _item.category_id database_2 _item.mandatory_code yes loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' replaces '_database.code_CSD' replaces '_database.code_ICSD' replaces '_database.code_MDF' replaces '_database.code_NBS' replaces '_database.code_PDF' replaces _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail CAS ; Chemical Abstracts ; CSD ; Cambridge Structural Database (organic and metal-organic compounds) ; ICSD ; Inorganic Crystal Structure Database ; MDF ; Metals Data File (metal structures) ; NDB ; Nucleic Acid Database ; NBS ; NBS (NIST) Crystal Data Database (lattice parameters) ; PDB ; Protein Data Bank ; PDF ; Powder Diffraction File (JCPDS/ICDD) ; RCSB ; Research Collaboratory for Structural Bioinformatics ; EBI ; European Bioinformatics Institute ; save_ save__database_2.database_code _item_description.description ; The code assigned by the database identified in _database_2.database_id. ; _item.name '_database_2.database_code' _item.category_id database_2 _item.mandatory_code yes loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' replaces '_database.code_CSD' replaces '_database.code_ICSD' replaces '_database.code_MDF' replaces '_database.code_NBS' replaces '_database.code_PDF' replaces _item_type.code line loop_ _item_examples.case 1ABC ABCDEF save_ ######################### ## DATABASE_PDB_CAVEAT ## ######################### save_database_PDB_caveat _category.description ; Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_caveat _category.mandatory_code no _category_key.name '_database_PDB_caveat.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _database_PDB_caveat.id _database_PDB_caveat.text 1 ; THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS ; 2 ; UNCORRECTABLE AT THIS TIME ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_caveat.id _item_description.description ; A unique identifier for the PDB caveat record. ; _item.name '_database_PDB_caveat.id' _item.category_id database_PDB_caveat _item.mandatory_code yes _item_type.code int save_ save__database_PDB_caveat.text _item_description.description ; The full text of the PDB caveat record. ; _item.name '_database_PDB_caveat.text' _item.category_id database_PDB_caveat _item.mandatory_code no _item_type.code text save_ ######################### ## DATABASE_PDB_MATRIX ## ######################### save_database_PDB_matrix _category.description ; The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_matrix _category.mandatory_code no _category_key.name '_database_PDB_matrix.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' save_ save__database_PDB_matrix.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_database_PDB_matrix.entry_id' _item.mandatory_code yes save_ save__database_PDB_matrix.origx[1][1] _item_description.description ; The [1][1] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[1][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[1][2] _item_description.description ; The [1][2] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[1][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[1][3] _item_description.description ; The [1][3] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[1][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[2][1] _item_description.description ; The [2][1] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[2][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[2][2] _item_description.description ; The [2][2] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[2][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[2][3] _item_description.description ; The [2][3] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[2][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[3][1] _item_description.description ; The [3][1] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[3][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[3][2] _item_description.description ; The [3][2] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[3][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx[3][3] _item_description.description ; The [3][3] element of the PDB ORIGX matrix. ; _item.name '_database_PDB_matrix.origx[3][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.origx_vector[1] _item_description.description ; The [1] element of the PDB ORIGX vector. ; _item.name '_database_PDB_matrix.origx_vector[1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.origx_vector[2] _item_description.description ; The [2] element of the PDB ORIGX vector. ; _item.name '_database_PDB_matrix.origx_vector[2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.origx_vector[3] _item_description.description ; The [3] element of the PDB ORIGX vector. ; _item.name '_database_PDB_matrix.origx_vector[3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.scale[1][1] _item_description.description ; The [1][1] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[1][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[1][2] _item_description.description ; The [1][2] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[1][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[1][3] _item_description.description ; The [1][3] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[1][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[2][1] _item_description.description ; The [2][1] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[2][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[2][2] _item_description.description ; The [2][2] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[2][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[2][3] _item_description.description ; The [2][3] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[2][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[3][1] _item_description.description ; The [3][1] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[3][1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[3][2] _item_description.description ; The [3][2] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[3][2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale[3][3] _item_description.description ; The [3][3] element of the PDB SCALE matrix. ; _item.name '_database_PDB_matrix.scale[3][3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_PDB_matrix.scale_vector[1] _item_description.description ; The [1] element of the PDB SCALE vector. ; _item.name '_database_PDB_matrix.scale_vector[1]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.scale_vector[2] _item_description.description ; The [2] element of the PDB SCALE vector. ; _item.name '_database_PDB_matrix.scale_vector[2]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_matrix.scale_vector[3] _item_description.description ; The [3] element of the PDB SCALE vector. ; _item.name '_database_PDB_matrix.scale_vector[3]' _item.category_id database_PDB_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ######################### ## DATABASE_PDB_REMARK ## ######################### save_database_PDB_remark _category.description ; Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_remark _category.mandatory_code no _category_key.name '_database_PDB_remark.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _database_PDB_remark.id _database_PDB_remark.text 3 ; REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE WEIGHTS OF THE CORRESPONDING RESTRAINTS) DISTANCE RESTRAINTS (ANGSTROMS) BOND DISTANCE 0.018(0.020) ANGLE DISTANCE 0.038(0.030) PLANAR 1-4 DISTANCE 0.043(0.040) PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) SINGLE TORSION CONTACT 0.216(0.500) MULTIPLE TORSION CONTACT 0.207(0.500) POSSIBLE HYDROGEN BOND 0.245(0.500) CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) PLANAR (OMEGA) 2.6(3.0) STAGGERED 17.4(15.0) ORTHONORMAL 18.1(20.0) ; 4 ; THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE THE CHAIN INDICATORS *A* AND *B*. ; # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_remark.id _item_description.description ; A unique identifier for the PDB remark record. ; _item.name '_database_PDB_remark.id' _item.category_id database_PDB_remark _item.mandatory_code yes _item_type.code int save_ save__database_PDB_remark.text _item_description.description ; The full text of the PDB remark record. ; _item.name '_database_PDB_remark.text' _item.category_id database_PDB_remark _item.mandatory_code no _item_type.code text save_ ###################### ## DATABASE_PDB_REV ## ###################### save_database_PDB_rev _category.description ; Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. ; _category.id database_PDB_rev _category.mandatory_code no _category_key.name '_database_PDB_rev.num' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _database_PDB_rev.num _database_PDB_rev.author_name _database_PDB_rev.date _database_PDB_rev.date_original _database_PDB_rev.status _database_PDB_rev.mod_type 1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30 'full release' 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_rev.author_name _item_description.description ; The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma precedes the first name(s) or initial(s). ; _item.name '_database_PDB_rev.author_name' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' save_ save__database_PDB_rev.date _item_description.description ; Date the PDB revision took place. Taken from the REVDAT record. ; _item.name '_database_PDB_rev.date' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save__database_PDB_rev.date_original _item_description.description ; Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record. ; _item.name '_database_PDB_rev.date_original' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case '1980-08-21' save_ save__database_PDB_rev.mod_type _item_description.description ; Taken from the REVDAT record. Refer to the Protein Data Bank format description at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html for details. ; _item.name '_database_PDB_rev.mod_type' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code int loop_ _item_enumeration.value _item_enumeration.detail 0 'initial entry' 1 'all other types of modification' 2 'modifications to CONECT records' 3 ; modifications affecting the coordinates or their transforms (CRYST1, ORIGX, SCALE, MTRIX, TVECT, ATOM, HETATM, SIGATM records) ; 4 ; layer 1 to layer 2 revision which may affect all record types ; 5 'data uniformity processing' save_ save__database_PDB_rev.num _item_description.description ; The value of _database_PDB_rev.num must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_database_PDB_rev.num' database_PDB_rev yes '_database_PDB_rev_record.rev_num' database_PDB_rev_record yes loop_ _item_linked.child_name _item_linked.parent_name '_database_PDB_rev_record.rev_num' '_database_PDB_rev.num' _item_type.code int save_ save__database_PDB_rev.replaced_by _item_description.description ; The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. ; _item.name '_database_PDB_rev.replaced_by' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line save_ save__database_PDB_rev.replaces _item_description.description ; The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. ; _item.name '_database_PDB_rev.replaces' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line save_ save__database_PDB_rev.status _item_description.description ; The status of this revision. ; _item.name '_database_PDB_rev.status' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value 'in preparation' 'prerelease' 'full release' 'obsolete' save_ ############################# ## DATABASE_PDB_REV_RECORD ## ############################# save_database_PDB_rev_record _category.description ; Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. ; _category.id database_PDB_rev_record _category.mandatory_code no loop_ _category_key.name '_database_PDB_rev_record.rev_num' '_database_PDB_rev_record.type' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _database_PDB_rev_record.rev_num _database_PDB_rev_record.type _database_PDB_rev_record.details 1 CONECT ; Error fix - incorrect connection between atoms 2312 and 2317 ; 2 MATRIX 'For consistency with 1995-08-04 style-guide' 3 ORIGX 'Based on new data from author' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_rev_record.details _item_description.description ; A description of special aspects of the revision of records in this PDB entry. ; _item.name '_database_PDB_rev_record.details' _item.category_id database_PDB_rev_record _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Based on new data from author' 'For consistency with 1995-08-04 style-guide' 'For consistency with structural class' save_ save__database_PDB_rev_record.rev_num _item_description.description ; This data item is a pointer to _database_PDB_rev.num in the DATABASE_PDB_REV category. ; _item.name '_database_PDB_rev_record.rev_num' _item.mandatory_code yes save_ save__database_PDB_rev_record.type _item_description.description ; The types of records that were changed in this revision to a PDB entry. ; _item.name '_database_PDB_rev_record.type' _item.category_id database_PDB_rev_record _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'CRYST1' 'SCALE' 'MTRIX' 'ATOM' 'HETATM' save_ ######################## ## DATABASE_PDB_TVECT ## ######################## save_database_PDB_tvect _category.description ; The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file. ; _category.id database_PDB_tvect _category.mandatory_code no _category_key.name '_database_PDB_tvect.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' save_ save__database_PDB_tvect.details _item_description.description ; A description of special aspects of this TVECT. ; _item.name '_database_PDB_tvect.details' _item.category_id database_PDB_tvect _item.mandatory_code no _item_type.code text save_ save__database_PDB_tvect.id _item_description.description ; The value of _database_PDB_tvect.id must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_database_PDB_tvect.id' _item.category_id database_PDB_tvect _item.mandatory_code yes _item_type.code code save_ save__database_PDB_tvect.vector[1] _item_description.description ; The [1] element of the PDB TVECT vector. ; _item.name '_database_PDB_tvect.vector[1]' _item.category_id database_PDB_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_tvect.vector[2] _item_description.description ; The [2] element of the PDB TVECT vector. ; _item.name '_database_PDB_tvect.vector[2]' _item.category_id database_PDB_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_PDB_tvect.vector[3] _item_description.description ; The [3] element of the PDB TVECT vector. ; _item.name '_database_PDB_tvect.vector[3]' _item.category_id database_PDB_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ############ ## DIFFRN ## ############ save_diffrn _category.description ; Data items in the DIFFRN category record details about the diffraction data and their measurement. ; _category.id diffrn _category.mandatory_code no _category_key.name '_diffrn.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn.id 'Set1' _diffrn.ambient_temp 293(3) _diffrn.ambient_environment ; Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air ; _diffrn.crystal_support ; 0.7 mm glass capillary, sealed with dental wax ; _diffrn.crystal_treatment ; Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn.id 'd1' _diffrn.details ; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per min. Background counts for 5 sec on each side every scan. ; _diffrn.ambient_temp 293 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn.ambient_environment _item_description.description ; The gas or liquid surrounding the sample, if not air. ; _item.name '_diffrn.ambient_environment' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_environment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ #save__diffrn.ambient_pressure # _item_description.description #; The mean pressure in kilopascals at which the intensities were # measured. #; # _item.name '_diffrn.ambient_pressure' # _item.category_id diffrn # _item.mandatory_code no # _item_aliases.alias_name '_diffrn_ambient_pressure' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_related.related_name '_diffrn.ambient_pressure_esd' # _item_related.function_code associated_esd # _item_type.code float # _item_type_conditions.code esd # _item_units.code kilopascals # save_ # #save__diffrn.ambient_pressure_esd # _item_description.description #; The standard uncertainty (estimated standard deviation) # of _diffrn.ambient_pressure. #; # _item.name '_diffrn.ambient_pressure_esd' # _item.category_id diffrn # _item.mandatory_code no # _item_default.value 0.0 # _item_related.related_name '_diffrn.ambient_pressure' # _item_related.function_code associated_value # _item_type.code float # _item_units.code kilopascals # save_ save__diffrn.ambient_temp _item_description.description ; The mean temperature in kelvins at which the intensities were measured. ; _item.name '_diffrn.ambient_temp' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_temperature' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_diffrn.ambient_temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvins save_ save__diffrn.ambient_temp_details _item_description.description ; A description of special aspects of temperature control during data collection. ; _item.name '_diffrn.ambient_temp_details' _item.category_id diffrn _item.mandatory_code no _item_type.code text save_ save__diffrn.ambient_temp_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _diffrn.ambient_temp. ; _item.name '_diffrn.ambient_temp_esd' _item.category_id diffrn _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvins save_ save__diffrn.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_diffrn.crystal_id' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_crystal_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn.crystal_support _item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '_diffrn.crystal_support' _item.category_id diffrn _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' save_ save__diffrn.crystal_treatment _item_description.description ; Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. ; _item.name '_diffrn.crystal_treatment' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_crystal_treatment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'equilibrated in hutch for 24 hours' 'flash frozen in liquid nitrogen' 'slow cooled with direct air stream' save_ save__diffrn.details _item_description.description ; Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. ; _item.name '_diffrn.details' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn.id _item_description.description ; This data item uniquely identifies a set of diffraction data. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn.id' diffrn yes '_diffrn_detector.diffrn_id' diffrn_detector yes '_diffrn_measurement.diffrn_id' diffrn_measurement yes '_diffrn_orient_matrix.diffrn_id' diffrn_orient_matrix yes '_diffrn_orient_refln.diffrn_id' diffrn_orient_refln yes '_diffrn_radiation.diffrn_id' diffrn_radiation yes '_diffrn_refln.diffrn_id' diffrn_refln yes '_diffrn_reflns.diffrn_id' diffrn_reflns yes '_diffrn_source.diffrn_id' diffrn_source yes '_diffrn_standard_refln.diffrn_id' diffrn_standard_refln yes '_diffrn_standards.diffrn_id' diffrn_standards yes loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_detector.diffrn_id' '_diffrn.id' '_diffrn_measurement.diffrn_id' '_diffrn.id' '_diffrn_orient_matrix.diffrn_id' '_diffrn.id' '_diffrn_orient_refln.diffrn_id' '_diffrn.id' '_diffrn_radiation.diffrn_id' '_diffrn.id' '_diffrn_refln.diffrn_id' '_diffrn.id' '_diffrn_reflns.diffrn_id' '_diffrn.id' '_diffrn_source.diffrn_id' '_diffrn.id' '_diffrn_standard_refln.diffrn_id' '_diffrn.id' '_diffrn_standards.diffrn_id' '_diffrn.id' _item_type.code code save_ ####################### ## DIFFRN_ATTENUATOR ## ####################### save_diffrn_attenuator _category.description ; Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. ; _category.id diffrn_attenuator _category.mandatory_code no _category_key.name '_diffrn_attenuator.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_attenuator.code 1 _diffrn_attenuator.scale 16.976 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_attenuator.code _item_description.description ; A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln.attenuator_code which is stored with the diffraction data. See _diffrn_attenuator.scale. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_attenuator.code' diffrn_attenuator yes _item_aliases.alias_name '_diffrn_attenuator_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.attenuator_code' '_diffrn_attenuator.code' _item_type.code code save_ save__diffrn_attenuator.scale _item_description.description ; The scale factor applied when an intensity measurement is reduced by an attenuator identified by _diffrn_attenuator.code. The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities. ; _item.name '_diffrn_attenuator.scale' _item.category_id diffrn_attenuator _item.mandatory_code no _item_aliases.alias_name '_diffrn_attenuator_scale' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ ##################### ## DIFFRN_DETECTOR ## ##################### save_diffrn_detector _category.description ; Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. ; _category.id diffrn_detector _category.mandatory_code no _category_key.name '_diffrn_detector.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_detector.diffrn_id 'd1' _diffrn_detector.detector 'multiwire' _diffrn_detector.type 'Siemens' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_detector.details _item_description.description ; A description of special aspects of the radiation detector. ; _item.name '_diffrn_detector.details' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn_detector.detector _item_description.description ; The general class of the radiation detector. ; _item.name '_diffrn_detector.detector' _item.category_id diffrn_detector _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_radiation_detector' cifdic.c91 1.0 '_diffrn_detector' cif_core.dic 2.0 _item_type.code text loop_ _item_examples.case 'photographic film' 'scintillation counter' 'CCD plate' 'BF~3~ counter' save_ save__diffrn_detector.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_detector.diffrn_id' _item.mandatory_code yes save_ #save__diffrn_detector.dtime # _item_description.description #; The deadtime in microseconds of the detectors used to measure # the diffraction intensities. #; # _item.name '_diffrn_detector.dtime' # _item.category_id diffrn_detector # _item.mandatory_code no # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version '_diffrn_radiation_detector_dtime' # cifdic.c91 # 1.0 # '_diffrn_detector_dtime' # cif_core.dic # 2.0 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_type.code float # _item_units.code microseconds # save_ save__diffrn_detector.type _item_description.description ; The make, model or name of the detector device used. ; _item.name '_diffrn_detector.type' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ######################## ## DIFFRN_MEASUREMENT ## ######################## save_diffrn_measurement _category.description ; Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. ; _category.id diffrn_measurement _category.mandatory_code no _category_key.name '_diffrn_measurement.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_measurement.diffrn_id 'd1' _diffrn_measurement.device '3-circle camera' _diffrn_measurement.device_type 'Supper model x' _diffrn_measurement.device_details 'none' _diffrn_measurement.method 'omega scan' _diffrn_measurement.details ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_measurement.diffrn_id 's1' _diffrn_measurement.device_type 'Philips PW1100/20 diffractometer' _diffrn_measurement.method \q/2\q ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_measurement.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_measurement.diffrn_id' _item.mandatory_code yes save_ save__diffrn_measurement.details _item_description.description ; A description of special aspects of the intensity measurement. ; _item.name '_diffrn_measurement.details' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; save_ save__diffrn_measurement.device _item_description.description ; The general class of goniometer or device used to support and orient the specimen. ; _item.name '_diffrn_measurement.device' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '3-circle camera' '4-circle camera' 'kappa-geometry camera' 'oscillation camera' 'precession camera' save_ save__diffrn_measurement.device_details _item_description.description ; A description of special aspects of the device used to measure the diffraction intensities. ; _item.name '_diffrn_measurement.device_details' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; commercial goniometer modified locally to allow for 90\% \t arc ; save_ save__diffrn_measurement.device_type _item_description.description ; The make, model or name of the measurement device (goniometer) used. ; _item.name '_diffrn_measurement.device_type' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Supper model q' 'Huber model r' 'Enraf-Nonius model s' 'homemade' save_ save__diffrn_measurement.method _item_description.description ; Method used to measure intensities. ; _item.name '_diffrn_measurement.method' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'profile data from theta/2theta scans' save_ save__diffrn_measurement.specimen_support _item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '_diffrn_measurement.specimen_support' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_specimen_support' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' save_ ########################## ## DIFFRN_ORIENT_MATRIX ## ########################## save_diffrn_orient_matrix _category.description ; Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data. ; _category.id diffrn_orient_matrix _category.mandatory_code no _category_key.name '_diffrn_orient_matrix.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. ; ; _diffrn_orient_matrix.diffrn_id set1 _diffrn_orient_matrix.type ; reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles ; _diffrn_orient_matrix.UB[1][1] -0.071479 _diffrn_orient_matrix.UB[1][2] 0.020208 _diffrn_orient_matrix.UB[1][3] 0.039076 _diffrn_orient_matrix.UB[2][1] 0.035372 _diffrn_orient_matrix.UB[2][2] 0.056209 _diffrn_orient_matrix.UB[2][3] 0.078324 _diffrn_orient_matrix.UB[3][1] -0.007470 _diffrn_orient_matrix.UB[3][2] 0.067854 _diffrn_orient_matrix.UB[3][3] -0.017832 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_orient_matrix.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_orient_matrix.diffrn_id' _item.mandatory_code yes save_ save__diffrn_orient_matrix.type _item_description.description ; A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. ; _item.name '_diffrn_orient_matrix.type' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn_orient_matrix.UB[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[1][1]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__diffrn_orient_matrix.UB[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[1][2]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[1][3]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[2][1]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[2][2]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[2][3]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[3][1]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[3][2]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_orient_matrix.UB[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type. ; _item.name '_diffrn_orient_matrix.UB[3][3]' _item.category_id diffrn_orient_matrix _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_matrix_UB_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ ######################### ## DIFFRN_ORIENT_REFLN ## ######################### save_diffrn_orient_refln _category.description ; Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities. ; _category.id diffrn_orient_refln _category.mandatory_code no loop_ _category_key.name '_diffrn_orient_refln.diffrn_id' '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_k' '_diffrn_orient_refln.index_l' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. ; ; _diffrn_orient_refln.diffrn_id myset1 _diffrn_orient_refln.index_h 2 _diffrn_orient_refln.index_k 0 _diffrn_orient_refln.index_l 2 _diffrn_orient_refln.angle_chi -28.45 _diffrn_orient_refln.angle_kappa -11.32 _diffrn_orient_refln.angle_omega 5.33 _diffrn_orient_refln.angle_phi 101.78 _diffrn_orient_refln.angle_psi 0.00 _diffrn_orient_refln.angle_theta 10.66 # ... data abbreviated ... ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_orient_refln.angle_chi _item_description.description ; Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_chi' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_chi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_kappa _item_description.description ; Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_kappa' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_kappa' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_omega _item_description.description ; Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_omega' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_omega' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_phi _item_description.description ; Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_phi' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_phi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_psi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_psi _item_description.description ; Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_psi' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_psi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_theta' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.angle_theta _item_description.description ; Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category. ; _item.name '_diffrn_orient_refln.angle_theta' _item.category_id diffrn_orient_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_orient_refln_angle_theta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.angle_chi' '_diffrn_orient_refln.angle_kappa' '_diffrn_orient_refln.angle_omega' '_diffrn_orient_refln.angle_phi' '_diffrn_orient_refln.angle_psi' _item_type.code float _item_units.code degrees save_ save__diffrn_orient_refln.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_orient_refln.diffrn_id' _item.mandatory_code yes save_ save__diffrn_orient_refln.index_h _item_description.description ; Miller index h of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_h' _item.category_id diffrn_orient_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_orient_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_k' '_diffrn_orient_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_orient_refln.index_k _item_description.description ; Miller index k of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_k' _item.category_id diffrn_orient_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_orient_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_orient_refln.index_l _item_description.description ; Miller index l of a reflection used to define the orientation matrix. ; _item.name '_diffrn_orient_refln.index_l' _item.category_id diffrn_orient_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_orient_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_orient_refln.index_h' '_diffrn_orient_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ ###################### ## DIFFRN_RADIATION ## ###################### save_diffrn_radiation _category.description ; Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. ; _category.id diffrn_radiation _category.mandatory_code no _category_key.name '_diffrn_radiation.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_radiation.diffrn_id 'set1' _diffrn_radiation.collimation '0.3 mm double pinhole' _diffrn_radiation.monochromator 'graphite' _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.wavelength_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_radiation.wavelength_id 1 _diffrn_radiation.type 'Cu K\a' _diffrn_radiation.monochromator 'graphite' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_radiation.collimation _item_description.description ; The collimation or focusing applied to the radiation. ; _item.name '_diffrn_radiation.collimation' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_collimation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '0.3 mm double-pinhole' '0.5 mm' 'focusing mirrors' save_ save__diffrn_radiation.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_radiation.diffrn_id' _item.mandatory_code yes save_ save__diffrn_radiation.filter_edge _item_description.description ; Absorption edge in angstroms of the radiation filter used. ; _item.name '_diffrn_radiation.filter_edge' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_filter_edge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_radiation.inhomogeneity _item_description.description ; Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. ; _item.name '_diffrn_radiation.inhomogeneity' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_inhomogeneity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__diffrn_radiation.monochromator _item_description.description ; The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. ; _item.name '_diffrn_radiation.monochromator' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_monochromator' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'Zr filter' 'Ge 220' 'none' 'equatorial mounted graphite' save_ save__diffrn_radiation.polarisn_norm _item_description.description ; The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See _diffrn_radiation.polarisn_ratio. ; _item.name '_diffrn_radiation.polarisn_norm' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_norm' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_radiation.polarisn_ratio _item_description.description ; Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized component of the radiation. The perpendicular component forms an angle of _diffrn_radiation.polarisn_norm to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). ; _item.name '_diffrn_radiation.polarisn_ratio' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_polarisn_ratio' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_radiation.probe _item_description.description ; The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined. ; _item.name '_diffrn_radiation.probe' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_probe' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value 'x-ray' 'neutron' 'electron' 'gamma' save_ save__diffrn_radiation.type _item_description.description ; The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. ; _item.name '_diffrn_radiation.type' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'CuK\a' 'Cu K\a~1~' 'Cu K-L~2,3~' 'white-beam' save_ save__diffrn_radiation.xray_symbol _item_description.description ; The IUPAC symbol for the X-ray wavelength for the probe radiation. ; _item.name '_diffrn_radiation.xray_symbol' _item.category_id diffrn_radiation _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_xray_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'K-L~3~' 'K\a~1~ in older Siegbahn notation' 'K-L~2~' 'K\a~2~ in older Siegbahn notation' 'K-M~3~' 'K\b~1~ in older Siegbahn notation' 'K-L~2,3~' 'use where K-L~3~ and K-L~2~ are not resolved' save_ save__diffrn_radiation.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation_wavelength.id in the DIFFRN_RADIATION_WAVELENGTH category. ; _item.name '_diffrn_radiation.wavelength_id' _item.mandatory_code yes save_ ################################# ## DIFFRN_RADIATION_WAVELENGTH ## ################################# save_diffrn_radiation_wavelength _category.description ; Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam. ; _category.id diffrn_radiation_wavelength _category.mandatory_code no _category_key.name '_diffrn_radiation_wavelength.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_radiation_wavelength.id _item_description.description ; The code identifying each value of _diffrn_radiation_wavelength.wavelength. Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The _diffrn_refln.wavelength_id codes must match one of the codes defined in this category. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_radiation_wavelength.id' diffrn_radiation_wavelength yes '_diffrn_radiation.wavelength_id' diffrn_radiation yes '_diffrn_refln.wavelength_id' diffrn_refln yes '_refln.wavelength_id' refln yes _item_aliases.alias_name '_diffrn_radiation_wavelength_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_radiation.wavelength_id' '_diffrn_radiation_wavelength.id' '_diffrn_refln.wavelength_id' '_diffrn_radiation_wavelength.id' '_refln.wavelength_id' '_diffrn_radiation_wavelength.id' _item_type.code code loop_ _item_examples.case 'x1' 'x2' 'neut' save_ save__diffrn_radiation_wavelength.wavelength _item_description.description ; The radiation wavelength in angstroms. ; _item.name '_diffrn_radiation_wavelength.wavelength' _item.category_id diffrn_radiation_wavelength _item.mandatory_code yes _item_aliases.alias_name '_diffrn_radiation_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_radiation_wavelength.wt _item_description.description ; The relative weight of a wavelength identified by the code _diffrn_radiation_wavelength.id in the list of wavelengths. ; _item.name '_diffrn_radiation_wavelength.wt' _item.category_id diffrn_radiation_wavelength _item.mandatory_code no _item_aliases.alias_name '_diffrn_radiation_wavelength_wt' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ ################## ## DIFFRN_REFLN ## ################## save_diffrn_refln _category.description ; Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by _diffrn_refln.diffrn_id. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by _diffrn_reflns.diffrn_id. ; _category.id diffrn_refln _category.mandatory_code no loop_ _category_key.name '_diffrn_refln.diffrn_id' '_diffrn_refln.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102. ; ; _diffrn_refln.diffrn_id set1 _diffrn_refln.id 1102 _diffrn_refln.wavelength_id Cu1fixed _diffrn_refln.angle_chi 32.21 _diffrn_refln.angle_kappa 20.12 _diffrn_refln.angle_omega 11.54 _diffrn_refln.angle_phi 176.02 _diffrn_refln.angle_psi 0.00 _diffrn_refln.angle_theta 23.08 _diffrn_refln.attenuator_code 'Ni.005' _diffrn_refln.counts_bg_1 22 _diffrn_refln.counts_bg_2 25 _diffrn_refln.counts_net 3450 _diffrn_refln.counts_peak 321 _diffrn_refln.counts_total 3499 _diffrn_refln.detect_slit_horiz 0.04 _diffrn_refln.detect_slit_vert 0.02 _diffrn_refln.elapsed_time 1.00 _diffrn_refln.index_h 4 _diffrn_refln.index_k 0 _diffrn_refln.index_l 2 _diffrn_refln.intensity_net 202.56 _diffrn_refln.intensity_sigma 2.18 _diffrn_refln.scale_group_code A24 _diffrn_refln.scan_mode om _diffrn_refln.scan_mode_backgd mo _diffrn_refln.scan_rate 1.2 _diffrn_refln.scan_time_backgd 900.00 _diffrn_refln.scan_width 1.0 _diffrn_refln.sint_over_lambda 0.25426 _diffrn_refln.standard_code 1 _diffrn_refln.wavelength 1.54184 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_refln.angle_chi _item_description.description ; The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_chi' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_chi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_kappa _item_description.description ; The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_kappa' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_kappa' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_omega _item_description.description ; The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_omega' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_omega' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_phi _item_description.description ; The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_phi' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_phi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_psi _item_description.description ; The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_psi' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_psi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.angle_theta _item_description.description ; The diffractometer angle theta of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. ; _item.name '_diffrn_refln.angle_theta' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_angle_theta' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.attenuator_code _item_description.description ; The code identifying the attenuator setting for this reflection. This code must match one of the _diffrn_attenuator.code values. ; _item.name '_diffrn_refln.attenuator_code' _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_attenuator_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn_refln.counts_bg_1 _item_description.description ; The diffractometer counts for the measurement of the background before the peak. ; _item.name '_diffrn_refln.counts_bg_1' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_bg_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_bg_2 _item_description.description ; The diffractometer counts for the measurement of the background after the peak. ; _item.name '_diffrn_refln.counts_bg_2' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_bg_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_net _item_description.description ; The diffractometer counts for the measurement of net counts after background removal. ; _item.name '_diffrn_refln.counts_net' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_net' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_peak _item_description.description ; The diffractometer counts for the measurement of counts for the peak scan or position. ; _item.name '_diffrn_refln.counts_peak' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_peak' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.counts_total _item_description.description ; The diffractometer counts for the measurement of total counts (background plus peak). ; _item.name '_diffrn_refln.counts_total' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_counts_total' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_refln.detect_slit_horiz _item_description.description ; Total slit aperture in degrees in the diffraction plane. ; _item.name '_diffrn_refln.detect_slit_horiz' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_horiz' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.detect_slit_vert _item_description.description ; Total slit aperture in degrees perpendicular to the diffraction plane. ; _item.name '_diffrn_refln.detect_slit_vert' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_detect_slit_vert' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_refln.diffrn_id' _item.mandatory_code yes save_ save__diffrn_refln.elapsed_time _item_description.description ; Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity. ; _item.name '_diffrn_refln.elapsed_time' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_elapsed_time' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code minutes save_ save__diffrn_refln.id _item_description.description ; The value of _diffrn_refln.id must uniquely identify the reflection in the data set identified by the item _diffrn_refln.diffrn_id. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_diffrn_refln.id' _item.category_id diffrn_refln _item.mandatory_code yes _item_type.code code save_ save__diffrn_refln.index_h _item_description.description ; Miller index h of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][]. ; _item.name '_diffrn_refln.index_h' _item.category_id diffrn_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_refln.index_k _item_description.description ; Miller index k of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][]. ; _item.name '_diffrn_refln.index_k' _item.category_id diffrn_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_refln.index_l _item_description.description ; Miller index l of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][]. ; _item.name '_diffrn_refln.index_l' _item.category_id diffrn_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_refln.index_h' '_diffrn_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_refln.intensity_net _item_description.description ; Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_net' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_intensity_net' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code float save_ save__diffrn_refln.intensity_sigma _item_description.description ; Standard uncertainty (estimated standard deviation) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_sigma' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_intensity_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code float save_ save__diffrn_refln.scale_group_code _item_description.description ; The code identifying the scale applying to this reflection. This data item is a pointer to _diffrn_scale_group.code in the DIFFRN_SCALE_GROUP category. ; _item.name '_diffrn_refln.scale_group_code' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn_refln.scan_mode _item_description.description ; The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. ; _item.name '_diffrn_refln.scan_mode' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_mode' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail om 'omega scan' ot 'omega/2theta scan' q 'Q scans (arbitrary reciprocal directions)' save_ save__diffrn_refln.scan_mode_backgd _item_description.description ; The code identifying the mode of scanning a reflection to measure the background intensity. ; _item.name '_diffrn_refln.scan_mode_backgd' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_mode_backgd' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail st 'stationary counter background' mo 'moving counter background' save_ save__diffrn_refln.scan_rate _item_description.description ; The rate of scanning a reflection in degrees per minute to measure the intensity. ; _item.name '_diffrn_refln.scan_rate' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_rate' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees_per_minute save_ save__diffrn_refln.scan_time_backgd _item_description.description ; The time spent measuring each background in seconds. ; _item.name '_diffrn_refln.scan_time_backgd' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_time_backgd' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code seconds save_ save__diffrn_refln.scan_width _item_description.description ; The scan width in degrees of the scan mode defined by the code _diffrn_refln.scan_mode. ; _item.name '_diffrn_refln.scan_width' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_scan_width' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_refln.sint_over_lambda _item_description.description ; The (sin theta)/lambda value in reciprocal angstroms for this reflection. ; _item.name '_diffrn_refln.sint_over_lambda' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_sint/lambda' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code reciprocal_angstroms save_ save__diffrn_refln.standard_code _item_description.description ; The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to _diffrn_standard_refln.code in the DIFFRN_STANDARD_REFLN category. ; _item.name '_diffrn_refln.standard_code' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_standard_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__diffrn_refln.wavelength _item_description.description ; The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. ; _item.name '_diffrn_refln.wavelength' _item.category_id diffrn_refln _item.mandatory_code no _item_aliases.alias_name '_diffrn_refln_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__diffrn_refln.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category. ; _item.name '_diffrn_refln.wavelength_id' _item.mandatory_code yes _item_aliases.alias_name '_diffrn_refln_wavelength_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ ################### ## DIFFRN_REFLNS ## ################### save_diffrn_reflns _category.description ; Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set. ; _category.id diffrn_reflns _category.mandatory_code no _category_key.name '_diffrn_reflns.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' # loop_ # _category_examples.detail # _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_reflns.av_R_equivalents _item_description.description ; The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average absolute difference between av(I) and the individual symmetry-equivalent intensities. ; _item.name '_diffrn_reflns.av_R_equivalents' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_R_equivalents' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_reflns.av_sigmaI_over_netI _item_description.description ; Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. ; _item.name '_diffrn_reflns.av_sigmaI_over_netI' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_av_sigmaI/netI' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__diffrn_reflns.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_reflns.diffrn_id' _item.mandatory_code yes save_ save__diffrn_reflns.limit_h_max _item_description.description ; The maximum value of the Miller index h for the reflection data specified by _diffrn_refln.index_h. ; _item.name '_diffrn_reflns.limit_h_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_h_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_h_min _item_description.description ; The minimum value of the Miller index h for the reflection data specified by _diffrn_refln.index_h. ; _item.name '_diffrn_reflns.limit_h_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_h_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_k_max _item_description.description ; The maximum value of the Miller index k for the reflection data specified by _diffrn_refln.index_k. ; _item.name '_diffrn_reflns.limit_k_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_k_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_k_min _item_description.description ; The minimum value of the Miller index k for the reflection data specified by _diffrn_refln.index_k. ; _item.name '_diffrn_reflns.limit_k_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_k_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_l_max _item_description.description ; The maximum value of the Miller index l for the reflection data specified by _diffrn_refln.index_l. ; _item.name '_diffrn_reflns.limit_l_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_l_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.limit_l_min _item_description.description ; The minimum value of the Miller index l for the reflection data specified by _diffrn_refln.index_l. ; _item.name '_diffrn_reflns.limit_l_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_limit_l_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__diffrn_reflns.number _item_description.description ; The total number of measured intensities, excluding reflections that are classified as systematically absent. ; _item.name '_diffrn_reflns.number' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_reflns.reduction_process _item_description.description ; A description of the process used to reduce the intensity data into structure-factor magnitudes. ; _item.name '_diffrn_reflns.reduction_process' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_reduction_process' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'data averaged using Fisher test' save_ save__diffrn_reflns.theta_max _item_description.description ; Maximum theta angle in degrees for the measured diffraction intensities. ; _item.name '_diffrn_reflns.theta_max' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_reflns.theta_min _item_description.description ; Minimum theta angle in degrees for the measured diffraction intensities. ; _item.name '_diffrn_reflns.theta_min' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_theta_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__diffrn_reflns.transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[1][1]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_11' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[1][2]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_12' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[1][3]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_13' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[2][1]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_21' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[2][2]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_22' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[2][3]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_23' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[3][1]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_31' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[3][2]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_32' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ save__diffrn_reflns.transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. ; _item.name '_diffrn_reflns.transf_matrix[3][3]' _item.category_id diffrn_reflns _item.mandatory_code no _item_aliases.alias_name '_diffrn_reflns_transf_matrix_33' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_sub_category.id matrix _item_type.code float save_ ######################## ## DIFFRN_SCALE_GROUP ## ######################## save_diffrn_scale_group _category.description ; Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set. ; _category.id diffrn_scale_group _category.mandatory_code no _category_key.name '_diffrn_scale_group.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. ; ; _diffrn_scale_group.code A24 _diffrn_scale_group.I_net 1.021 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_scale_group.code _item_description.description ; The value of _diffrn_scale_group.code must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_scale_group.code' diffrn_scale_group yes '_diffrn_refln.scale_group_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.scale_group_code' '_diffrn_scale_group.code' _item_type.code code loop_ _item_examples.case '1' '2' 'c1' 'c2' save_ save__diffrn_scale_group.I_net _item_description.description ; The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale. ; _item.name '_diffrn_scale_group.I_net' _item.category_id diffrn_scale_group _item.mandatory_code no _item_aliases.alias_name '_diffrn_scale_group_I_net' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################### ## DIFFRN_SOURCE ## ################### save_diffrn_source _category.description ; Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. ; _category.id diffrn_source _category.mandatory_code no _category_key.name '_diffrn_source.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _diffrn_source.diffrn_id 's1' _diffrn_source.source 'rotating anode' _diffrn_source.type 'Rigaku RU-200' _diffrn_source.power 50 _diffrn_source.current 180 _diffrn_source.size '8mm x 0.4 mm broad-focus' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_source.current _item_description.description ; The current in milliamperes at which the radiation source was operated. ; _item.name '_diffrn_source.current' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_current' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code milliamperes save_ save__diffrn_source.details _item_description.description ; A description of special aspects of the radiation source used. ; _item.name '_diffrn_source.details' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__diffrn_source.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_source.diffrn_id' _item.mandatory_code yes save_ save__diffrn_source.power _item_description.description ; The power in kilowatts at which the radiation source was operated. ; _item.name '_diffrn_source.power' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_power' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code kilowatts save_ save__diffrn_source.size _item_description.description ; The dimensions of the source as viewed from the sample. ; _item.name '_diffrn_source.size' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_size' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case '8mm x 0.4 mm fine-focus' 'broad focus' save_ save__diffrn_source.source _item_description.description ; The general class of the radiation source. ; _item.name '_diffrn_source.source' _item.category_id diffrn_source _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_radiation_source' cifdic.c91 1.0 '_diffrn_source' cif_core.dic 2.0 _item_type.code text loop_ _item_examples.case 'sealed X-ray tube' 'nuclear reactor' 'spallation source' 'electron microscope' 'rotating-anode X-ray tube' 'synchrotron' save_ save__diffrn_source.target _item_description.description ; The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources. ; _item.name '_diffrn_source.target' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_target' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_enumeration.value H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr save_ save__diffrn_source.type _item_description.description ; The make, model or name of the source of radiation. ; _item.name '_diffrn_source.type' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'NSLS beamline X8C' 'Rigaku RU200' save_ save__diffrn_source.voltage _item_description.description ; The voltage in kilovolts at which the radiation source was operated. ; _item.name '_diffrn_source.voltage' _item.category_id diffrn_source _item.mandatory_code no _item_aliases.alias_name '_diffrn_source_voltage' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code kilovolts save_ ########################### ## DIFFRN_STANDARD_REFLN ## ########################### save_diffrn_standard_refln _category.description ; Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. ; _category.id diffrn_standard_refln _category.mandatory_code no loop_ _category_key.name '_diffrn_standard_refln.diffrn_id' '_diffrn_standard_refln.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _diffrn_standard_refln.diffrn_id _diffrn_standard_refln.code _diffrn_standard_refln.index_h _diffrn_standard_refln.index_k _diffrn_standard_refln.index_l s1 1 3 2 4 s1 1 1 9 1 s1 1 3 0 10 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_standard_refln.code _item_description.description ; The code identifying a reflection measured as a standard reflection with the indices _diffrn_standard_refln.index_h, _diffrn_standard_refln.index_k and _diffrn_standard_refln.index_l. This is the same code as the _diffrn_refln.standard_code in the DIFFRN_REFLN list. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_standard_refln.code' diffrn_standard_refln yes '_diffrn_refln.standard_code' diffrn_refln yes _item_aliases.alias_name '_diffrn_standard_refln_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.standard_code' '_diffrn_standard_refln.code' _item_type.code code loop_ _item_examples.case '1' '2' 'c1' 'c2' save_ save__diffrn_standard_refln.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_standard_refln.diffrn_id' _item.mandatory_code yes save_ save__diffrn_standard_refln.index_h _item_description.description ; Miller index h of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_h' _item.category_id diffrn_standard_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_standard_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_k' '_diffrn_standard_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_standard_refln.index_k _item_description.description ; Miller index k of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_k' _item.category_id diffrn_standard_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_standard_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_h' '_diffrn_standard_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__diffrn_standard_refln.index_l _item_description.description ; Miller index l of a standard reflection used in the diffraction measurement process. ; _item.name '_diffrn_standard_refln.index_l' _item.category_id diffrn_standard_refln _item.mandatory_code yes _item_aliases.alias_name '_diffrn_standard_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_diffrn_standard_refln.index_h' '_diffrn_standard_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ ###################### ## DIFFRN_STANDARDS ## ###################### save_diffrn_standards _category.description ; Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. ; _category.id diffrn_standards _category.mandatory_code no _category_key.name '_diffrn_standards.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _diffrn_standards.diffrn_id 's1' _diffrn_standards.number 3 _diffrn_standards.interval_time 120 _diffrn_standards.decay_% 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_standards.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_standards.diffrn_id' _item.mandatory_code yes save_ save__diffrn_standards.decay_% _item_description.description ; The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. ; _item.name '_diffrn_standards.decay_%' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_decay_%' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 100.0 100.0 100.0 . _item_type.code float save_ save__diffrn_standards.interval_count _item_description.description ; The number of reflection intensities between the measurement of standard reflection intensities. ; _item.name '_diffrn_standards.interval_count' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_interval_count' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_standards.interval_time _item_description.description ; The time in minutes between the measurement of standard reflection intensities. ; _item.name '_diffrn_standards.interval_time' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_interval_time' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code float _item_units.code minutes save_ save__diffrn_standards.number _item_description.description ; The number of unique standard reflections used during the measurement of the diffraction intensities. ; _item.name '_diffrn_standards.number' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__diffrn_standards.scale_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of the individual mean standard scales applied to the intensity data. ; _item.name '_diffrn_standards.scale_sigma' _item.category_id diffrn_standards _item.mandatory_code no _item_aliases.alias_name '_diffrn_standards_scale_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ############ ## ENTITY ## ############ save_entity _category.description ; Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. ; _category.id entity _category.mandatory_code no _category_key.name '_entity.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity.id _entity.type _entity.formula_weight _entity.details 1 polymer 10916 ; The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer. ; 2 non-polymer '762' . 3 water 18 . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity.details _item_description.description ; A description of special aspects of the entity. ; _item.name '_entity.details' _item.category_id entity _item.mandatory_code no _item_type.code text save_ save__entity.formula_weight _item_description.description ; Formula mass in daltons of the entity. ; _item.name '_entity.formula_weight' _item.category_id entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__entity.id _item_description.description ; The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity.id' entity yes '_atom_site.label_entity_id' atom_site no '_entity_keywords.entity_id' entity_keywords yes '_entity_link.entity_id_1' entity_link yes '_entity_link.entity_id_2' entity_link yes '_entity_name_com.entity_id' entity_name_com yes '_entity_name_sys.entity_id' entity_name_sys yes '_entity_poly.entity_id' entity_poly yes '_entity_poly_seq.entity_id' entity_poly_seq yes '_entity_src_gen.entity_id' entity_src_gen yes '_entity_src_nat.entity_id' entity_src_nat yes '_struct_asym.entity_id' struct_asym yes '_struct_ref.entity_id' struct_ref yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_entity_id' '_entity.id' '_entity_keywords.entity_id' '_entity.id' '_entity_link.entity_id_1' '_entity.id' '_entity_link.entity_id_2' '_entity.id' '_entity_name_com.entity_id' '_entity.id' '_entity_name_sys.entity_id' '_entity.id' '_entity_poly.entity_id' '_entity.id' '_entity_poly_seq.entity_id' '_entity_poly.entity_id' '_entity_src_gen.entity_id' '_entity.id' '_entity_src_nat.entity_id' '_entity.id' '_struct_asym.entity_id' '_entity.id' '_struct_ref.entity_id' '_entity.id' save_ save__entity.src_method _item_description.description ; The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. ; _item.name '_entity.src_method' _item.category_id entity _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail nat ; entity isolated from a natural source ; man ; entity isolated from a genetically manipulated source ; syn ; entity obtained synthetically ; save_ save__entity.type _item_description.description ; Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. ; _item.name '_entity.type' _item.category_id entity _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail polymer 'entity is a polymer' non-polymer 'entity is not a polymer' water 'water in the solvent model' save_ ##################### ## ENTITY_KEYWORDS ## ##################### save_entity_keywords _category.description ; Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA. ; _category.id entity_keywords _category.mandatory_code no loop_ _category_key.name '_entity_keywords.entity_id' '_entity_keywords.text' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_keywords.entity_id _entity_keywords.text 1 'polypeptide' 2 'natural product, inhibitor, reduced peptide' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_keywords.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_keywords.entity_id' _item.mandatory_code yes save_ save__entity_keywords.text _item_description.description ; Keywords describing this entity. ; _item.name '_entity_keywords.text' _item.category_id entity_keywords _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'polypeptide' 'natural product' 'polysaccharide' save_ ################# ## ENTITY_LINK ## ################# save_entity_link _category.description ; Data items in the ENTITY_LINK category give details about the links between entities. ; _category.id entity_link _category.mandatory_code no _category_key.name '_entity_link.link_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' save_ save__entity_link.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_entity_link.link_id' _item.mandatory_code yes save_ save__entity_link.details _item_description.description ; A description of special aspects of a link between chemical components in the structure. ; _item.name '_entity_link.details' _item.category_id entity_link _item.mandatory_code no _item_type.code text save_ save__entity_link.entity_id_1 _item_description.description ; The entity ID of the first of the two entities joined by the link. This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_link.entity_id_1' _item.mandatory_code yes save_ save__entity_link.entity_id_2 _item_description.description ; The entity ID of the second of the two entities joined by the link. This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_link.entity_id_2' _item.mandatory_code yes save_ save__entity_link.entity_seq_num_1 _item_description.description ; For a polymer entity, the sequence number in the first of the two entities containing the link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_entity_link.entity_seq_num_1' _item.mandatory_code no save_ save__entity_link.entity_seq_num_2 _item_description.description ; For a polymer entity, the sequence number in the second of the two entities containing the link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_entity_link.entity_seq_num_2' _item.mandatory_code no save_ ##################### ## ENTITY_NAME_COM ## ##################### save_entity_name_com _category.description ; Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin. ; _category.id entity_name_com _category.mandatory_code no loop_ _category_key.name '_entity_name_com.entity_id' '_entity_name_com.name' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_name_com.entity_id _entity_name_com.name 1 'HIV-1 protease monomer' 1 'HIV-1 PR monomer' 2 'acetyl-pepstatin' 2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine' 3 'water' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_name_com.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_name_com.entity_id' _item.mandatory_code yes save_ save__entity_name_com.name _item_description.description ; A common name for the entity. ; _item.name '_entity_name_com.name' _item.category_id entity_name_com _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'HIV protease monomer' 'hemoglobin alpha chain' '2-fluoro-1,4-dichloro benzene' 'arbutin' save_ ##################### ## ENTITY_NAME_SYS ## ##################### save_entity_name_sys _category.description ; Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. ; _category.id entity_name_sys _category.mandatory_code no loop_ _category_key.name '_entity_name_sys.entity_id' '_entity_name_sys.name' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_name_sys.entity_id _entity_name_sys.name 1 'EC 3.4.23.16' 2 'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta' 3 water ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_name_sys.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_name_sys.entity_id' _item.mandatory_code yes save_ save__entity_name_sys.name _item_description.description ; The systematic name for the entity. ; _item.name '_entity_name_sys.name' _item.category_id entity_name_sys _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'hydroquinone-beta-D-pyranoside' 'EC 2.1.1.1' '2-fluoro-1,4-dichlorobenzene' save_ save__entity_name_sys.system _item_description.description ; The system used to generate the systematic name of the entity. ; _item.name '_entity_name_sys.system' _item.category_id entity_name_sys _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Chemical Abstracts conventions' 'enzyme convention' 'Sigma catalog' save_ ################# ## ENTITY_POLY ## ################# save_entity_poly _category.description ; Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. ; _category.id entity_poly _category.mandatory_code no _category_key.name '_entity_poly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_chirality _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.type_details 1 polypeptide(L) no no no . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_poly.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_poly.entity_id' _item.mandatory_code yes save_ save__entity_poly.nstd_chirality _item_description.description ; A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in _entity_poly.type. ; _item.name '_entity_poly.nstd_chirality' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no ; polymer contains no monomers with different chirality ; n ; abbreviation for "no" ; yes ; polymer contains at least one monomer with different chirality ; y ; abbreviation for "yes" ; save_ save__entity_poly.nstd_linkage _item_description.description ; A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by _entity_poly.type. ; _item.name '_entity_poly.nstd_linkage' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'polymer contains no different links' n 'abbreviation for "no"' yes ; polymer contains at least one different link ; y 'abbreviation for "yes"' save_ save__entity_poly.nstd_monomer _item_description.description ; A flag to indicate whether the polymer contains at least one monomer that is not considered standard. ; _item.name '_entity_poly.nstd_monomer' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'polymer contains no nonstandard monomers' n 'abbreviation for "no"' yes ; polymer contains at least one nonstandard monomer ; y 'abbreviation for "yes"' save_ save__entity_poly.number_of_monomers _item_description.description ; The number of monomers in the polymer. ; _item.name '_entity_poly.number_of_monomers' _item.category_id entity_poly _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__entity_poly.type _item_description.description ; The type of the polymer. ; _item.name '_entity_poly.type' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value 'polypeptide(D)' 'polypeptide(L)' 'polydeoxyribonucleotide' 'polyribonucleotide' 'polysaccharide(D)' 'polysaccharide(L)' 'other' save_ save__entity_poly.type_details _item_description.description ; A description of special aspects of the polymer type. ; _item.name '_entity_poly.type_details' _item.category_id entity_poly _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'monomer Ala 16 is a D-amino acid' 'the oligomer contains alternating RNA and DNA units' save_ ##################### ## ENTITY_POLY_SEQ ## ##################### save_entity_poly_seq _category.description ; Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. ; _category.id entity_poly_seq _category.mandatory_code no loop_ _category_key.name '_entity_poly_seq.entity_id' '_entity_poly_seq.num' '_entity_poly_seq.mon_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU 1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU 1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE 1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS 1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_poly_seq.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_poly_seq.entity_id' _item.mandatory_code yes save_ save__entity_poly_seq.hetero _item_description.description ; A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. This would be rare. ; _item.name '_entity_poly_seq.hetero' _item.category_id entity_poly_seq _item.mandatory_code no _item_default.value no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'sequence is not heterogeneous at this monomer' n 'abbreviation for "no"' yes 'sequence is heterogeneous at this monomer' y 'abbreviation for "yes"' save_ save__entity_poly_seq.mon_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_entity_poly_seq.mon_id' _item.mandatory_code yes save_ save__entity_poly_seq.num _item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_poly_seq.num' entity_poly_seq yes '_atom_site.label_seq_id' atom_site no '_entity_link.entity_seq_num_1' entity_link no '_entity_link.entity_seq_num_2' entity_link no '_geom_angle.atom_site_label_seq_id_1' geom_angle no '_geom_angle.atom_site_label_seq_id_2' geom_angle no '_geom_angle.atom_site_label_seq_id_3' geom_angle no '_geom_bond.atom_site_label_seq_id_1' geom_bond no '_geom_bond.atom_site_label_seq_id_2' geom_bond no '_geom_contact.atom_site_label_seq_id_1' geom_contact no '_geom_contact.atom_site_label_seq_id_2' geom_contact no '_geom_hbond.atom_site_label_seq_id_A' geom_hbond no '_geom_hbond.atom_site_label_seq_id_D' geom_hbond no '_geom_hbond.atom_site_label_seq_id_H' geom_hbond no '_geom_torsion.atom_site_label_seq_id_1' geom_torsion no '_geom_torsion.atom_site_label_seq_id_2' geom_torsion no '_geom_torsion.atom_site_label_seq_id_3' geom_torsion no '_geom_torsion.atom_site_label_seq_id_4' geom_torsion no '_struct_conf.beg_label_seq_id' struct_conf yes '_struct_conf.end_label_seq_id' struct_conf yes '_struct_conn.ptnr1_label_seq_id' struct_conn yes '_struct_conn.ptnr2_label_seq_id' struct_conn yes '_struct_mon_nucl.label_seq_id' struct_mon_nucl yes '_struct_mon_prot.label_seq_id' struct_mon_prot yes '_struct_mon_prot_cis.label_seq_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_seq_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_seq_id' struct_ncs_dom_lim yes '_struct_ref_seq.seq_align_beg' struct_ref_seq yes '_struct_ref_seq.seq_align_end' struct_ref_seq yes '_struct_ref_seq_dif.seq_num' struct_ref_seq_dif yes '_struct_sheet_hbond.range_1_beg_label_seq_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_1_end_label_seq_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_beg_label_seq_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_end_label_seq_id' struct_sheet_hbond yes '_struct_sheet_range.beg_label_seq_id' struct_sheet_range yes '_struct_sheet_range.end_label_seq_id' struct_sheet_range yes '_struct_site_gen.label_seq_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_seq_id' '_entity_poly_seq.num' '_entity_link.entity_seq_num_1' '_entity_poly_seq.num' '_entity_link.entity_seq_num_2' '_entity_poly_seq.num' '_geom_angle.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_angle.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_angle.atom_site_label_seq_id_3' '_atom_site.label_seq_id' '_geom_bond.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_bond.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_contact.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_contact.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_hbond.atom_site_label_seq_id_A' '_atom_site.label_seq_id' '_geom_hbond.atom_site_label_seq_id_D' '_atom_site.label_seq_id' '_geom_hbond.atom_site_label_seq_id_H' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_1' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_2' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_3' '_atom_site.label_seq_id' '_geom_torsion.atom_site_label_seq_id_4' '_atom_site.label_seq_id' '_struct_conf.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_conf.end_label_seq_id' '_atom_site.label_seq_id' '_struct_conn.ptnr1_label_seq_id' '_atom_site.label_seq_id' '_struct_conn.ptnr2_label_seq_id' '_atom_site.label_seq_id' '_struct_mon_nucl.label_seq_id' '_atom_site.label_seq_id' '_struct_mon_prot.label_seq_id' '_atom_site.label_seq_id' '_struct_mon_prot_cis.label_seq_id' '_atom_site.label_seq_id' '_struct_ncs_dom_lim.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_ncs_dom_lim.end_label_seq_id' '_atom_site.label_seq_id' '_struct_ref_seq.seq_align_beg' '_entity_poly_seq.num' '_struct_ref_seq.seq_align_end' '_entity_poly_seq.num' '_struct_ref_seq_dif.seq_num' '_entity_poly_seq.num' '_struct_sheet_hbond.range_1_beg_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_hbond.range_1_end_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_hbond.range_2_beg_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_hbond.range_2_end_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_range.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_sheet_range.end_label_seq_id' '_atom_site.label_seq_id' '_struct_site_gen.label_seq_id' '_atom_site.label_seq_id' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ #################### ## ENTITY_SRC_GEN ## #################### save_entity_src_gen _category.description ; Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). ; _category.id entity_src_gen _category.mandatory_code no _category_key.name '_entity_src_gen.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_src_gen.entity_id _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.host_org_common_name _entity_src_gen.host_org_genus _entity_src_gen.host_org_species _entity_src_gen.plasmid_name 1 'HIV-1' '?' '?' 'NY-5' 'bacteria' 'Escherichia' 'coli' 'pB322' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_src_gen.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_src_gen.entity_id' _item.mandatory_code yes save_ save__entity_src_gen.gene_src_common_name _item_description.description ; The common name of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_common_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'man' 'yeast' 'bacteria' save_ save__entity_src_gen.gene_src_details _item_description.description ; A description of special aspects of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.gene_src_genus _item_description.description ; The genus of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_genus' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia' save_ save__entity_src_gen.gene_src_species _item_description.description ; The species of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_species' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli' save_ save__entity_src_gen.gene_src_strain _item_description.description ; The strain of the natural organism from which the gene was obtained, if relevant. ; _item.name '_entity_src_gen.gene_src_strain' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_gen.gene_src_tissue _item_description.description ; The tissue of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_tissue' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__entity_src_gen.gene_src_tissue_fraction _item_description.description ; The subcellular fraction of the tissue of the natural organism from which the gene was obtained. ; _item.name '_entity_src_gen.gene_src_tissue_fraction' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane' save_ save__entity_src_gen.host_org_common_name _item_description.description ; The common name of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_common_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'yeast' 'bacteria' save_ save__entity_src_gen.host_org_details _item_description.description ; A description of special aspects of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.host_org_genus _item_description.description ; The genus of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_genus' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Saccharomyces' 'Escherichia' save_ save__entity_src_gen.host_org_species _item_description.description ; The species of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_species' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'cerevisiae' 'coli' save_ save__entity_src_gen.host_org_strain _item_description.description ; The strain of the organism that served as host for the production of the entity. ; _item.name '_entity_src_gen.host_org_strain' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_gen.plasmid_details _item_description.description ; A description of special aspects of the plasmid that produced the entity in the host organism. ; _item.name '_entity_src_gen.plasmid_details' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text save_ save__entity_src_gen.plasmid_name _item_description.description ; The name of the plasmid that produced the entity in the host organism. ; _item.name '_entity_src_gen.plasmid_name' _item.category_id entity_src_gen _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'pET3C' 'pT123sab' save_ #################### ## ENTITY_SRC_NAT ## #################### save_entity_src_nat _category.description ; Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue. ; _category.id entity_src_nat _category.mandatory_code no _category_key.name '_entity_src_nat.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _entity_src_nat.entity_id _entity_src_nat.common_name _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.details 2 'bacteria' 'Actinomycetes' '?' ; Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_src_nat.common_name _item_description.description ; The common name of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.common_name' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'man' 'yeast' 'bacteria' save_ save__entity_src_nat.details _item_description.description ; A description of special aspects of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.details' _item.category_id entity_src_nat _item.mandatory_code no _item_type.code text save_ save__entity_src_nat.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_src_nat.entity_id' _item.mandatory_code yes save_ save__entity_src_nat.genus _item_description.description ; The genus of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.genus' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'Homo' 'Saccharomyces' 'Escherichia' save_ save__entity_src_nat.species _item_description.description ; The species of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.species' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'sapiens' 'cerevisiae' 'coli' save_ save__entity_src_nat.strain _item_description.description ; The strain of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.strain' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'DH5a' 'BMH 71-18' save_ save__entity_src_nat.tissue _item_description.description ; The tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'heart' 'liver' 'eye lens' save_ save__entity_src_nat.tissue_fraction _item_description.description ; The subcellular fraction of the tissue of the organism from which the entity was isolated. ; _item.name '_entity_src_nat.tissue_fraction' _item.category_id entity_src_nat _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'mitochondria' 'nucleus' 'membrane' save_ ########### ## ENTRY ## ########### save_entry _category.description ; There is only one item in the ENTRY category, _entry.id. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. ; _category.id entry _category.mandatory_code no _category_key.name '_entry.id' loop_ _category_group.id 'inclusive_group' 'entry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _entry.id '5HVP' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _entry.id 'TOZ' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entry.id _item_description.description ; The value of _entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entry.id' entry yes '_atom_sites.entry_id' atom_sites yes '_cell.entry_id' cell yes '_cell_measurement.entry_id' cell_measurement yes '_chemical.entry_id' chemical yes '_chemical_formula.entry_id' chemical_formula yes '_computing.entry_id' computing yes '_database.entry_id' database yes '_database_PDB_matrix.entry_id' database_PDB_matrix yes '_entry_link.entry_id' entry_link yes '_exptl.entry_id' exptl yes '_geom.entry_id' geom yes '_journal.entry_id' journal yes '_phasing_averaging.entry_id' phasing_averaging yes '_phasing_isomorphous.entry_id' phasing_isomorphous yes '_phasing_MAD.entry_id' phasing_MAD yes '_phasing_MIR.entry_id' phasing_MIR yes '_publ.entry_id' publ yes '_publ_manuscript_incl.entry_id' publ_manuscript_incl yes '_refine.entry_id' refine yes '_refine_analyze.entry_id' refine_analyze yes '_reflns.entry_id' reflns yes '_struct.entry_id' struct yes '_struct_keywords.entry_id' struct_keywords yes '_struct_mon_details.entry_id' struct_mon_details yes '_symmetry.entry_id' symmetry yes _item_aliases.alias_name '_audit_block_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites.entry_id' '_entry.id' '_cell.entry_id' '_entry.id' '_cell_measurement.entry_id' '_entry.id' '_chemical.entry_id' '_entry.id' '_chemical_formula.entry_id' '_entry.id' '_computing.entry_id' '_entry.id' '_database.entry_id' '_entry.id' '_database_PDB_matrix.entry_id' '_entry.id' '_entry_link.entry_id' '_entry.id' '_exptl.entry_id' '_entry.id' '_geom.entry_id' '_entry.id' '_journal.entry_id' '_entry.id' '_phasing_averaging.entry_id' '_entry.id' '_phasing_isomorphous.entry_id' '_entry.id' '_phasing_MAD.entry_id' '_entry.id' '_phasing_MIR.entry_id' '_entry.id' '_publ.entry_id' '_entry.id' '_publ_manuscript_incl.entry_id' '_entry.id' '_refine.entry_id' '_entry.id' '_refine_analyze.entry_id' '_entry.id' '_reflns.entry_id' '_entry.id' '_struct.entry_id' '_entry.id' '_struct_keywords.entry_id' '_entry.id' '_struct_mon_details.entry_id' '_entry.id' '_symmetry.entry_id' '_entry.id' _item_type.code code save_ save_entry_link _category.description ; Data items in the ENTRY_LINK category record the relationships between the current data block identified by _entry.id and other data blocks within the current file which may be referenced in the current data block. ; _category.id entry_link _category.mandatory_code no loop_ _category_key.name '_entry_link.id' '_entry_link.entry_id' loop_ _category_group.id 'inclusive_group' 'entry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; ; loop_ _entry_link.id _entry_link.entry_id _entry_link.details KSE_COM KSE_TEXT 'experimental data common to ref./mod. structures' KSE_REF KSE_TEXT 'reference structure' KSE_MOD KSE_TEXT 'modulated structure' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entry_link.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_entry_link.entry_id' _item.mandatory_code yes save_ save__entry_link.id _item_description.description ; The value of _entry_link.id identifies a data block related to the current data block. ; _item.name '_entry_link.id' _item.category_id entry_link _item.mandatory_code yes _item_aliases.alias_name '_audit_link_block_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__entry_link.details _item_description.description ; A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. ; _item.name '_entry_link.details' _item.category_id entry_link _item.mandatory_code no _item_aliases.alias_name '_audit_link_block_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ########### ## EXPTL ## ########### save_exptl _category.description ; Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. ; _category.id exptl _category.mandatory_code no _category_key.name '_exptl.entry_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. ; ; _exptl.entry_id datablock1 _exptl.absorpt_coefficient_mu 1.22 _exptl.absorpt_correction_T_max 0.896 _exptl.absorpt_correction_T_min 0.802 _exptl.absorpt_correction_type integration _exptl.absorpt_process_details ; Gaussian grid method from SHELX76 Sheldrick, G. M., "SHELX-76: structure determination and refinement program", Cambridge University, UK, 1976 ; _exptl.crystals_number 1 _exptl.details ; Enraf-Nonius LT2 liquid nitrogen variable-temperature device used ; _exptl.method 'single-crystal x-ray diffraction' _exptl.method_details ; graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl.absorpt_coefficient_mu _item_description.description ; The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. ; _item.name '_exptl.absorpt_coefficient_mu' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_coefficient_mu' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code reciprocal_millimetres save_ save__exptl.absorpt_correction_T_max _item_description.description ; The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. ; _item.name '_exptl.absorpt_correction_T_max' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_T_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__exptl.absorpt_correction_T_min _item_description.description ; The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. ; _item.name '_exptl.absorpt_correction_T_min' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_T_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__exptl.absorpt_correction_type _item_description.description ; The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. ; _item.name '_exptl.absorpt_correction_type' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_correction_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail analytical 'analytical from crystal shape' cylinder 'cylindrical' empirical 'empirical from intensities' gaussian 'Gaussian from crystal shape' integration 'integration from crystal shape' multi-scan 'symmetry-related measurements' none 'no correction applied' numerical 'numerical from crystal shape' psi-scan 'psi-scan corrections' refdelf 'refined from delta-F' sphere 'spherical' save_ save__exptl.absorpt_process_details _item_description.description ; Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. ; _item.name '_exptl.absorpt_process_details' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_absorpt_process_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Tompa analytical' save_ save__exptl.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_exptl.entry_id' _item.mandatory_code yes save_ save__exptl.crystals_number _item_description.description ; The total number of crystals used in the measurement of intensities. ; _item.name '_exptl.crystals_number' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_crystals_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__exptl.details _item_description.description ; Any special information about the experimental work prior to the intensity measurement. See also _exptl_crystal.preparation. ; _item.name '_exptl.details' _item.category_id exptl _item.mandatory_code no _item_aliases.alias_name '_exptl_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__exptl.method _item_description.description ; The method used in the experiment. ; _item.name '_exptl.method' _item.category_id exptl _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'single-crystal x-ray diffraction' 'single-crystal neutron diffraction' 'single-crystal electron diffraction' 'fiber x-ray diffraction' 'fiber neutron diffraction' 'fiber electron diffraction' 'single-crystal joint x-ray and neutron diffraction' 'single-crystal joint x-ray and electron diffraction' 'solution nmr' 'solid-state nmr' 'theoretical model' 'other' save_ save__exptl.method_details _item_description.description ; A description of special aspects of the experimental method. ; _item.name '_exptl.method_details' _item.category_id exptl _item.mandatory_code no _item_type.code text loop_ _item_examples.case '29 structures' 'minimized average structure' save_ ################### ## EXPTL_CRYSTAL ## ################### save_exptl_crystal _category.description ; Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density. ; _category.id exptl_crystal _category.mandatory_code no _category_key.name '_exptl_crystal.id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. ; ; _exptl_crystal.id xst2l _exptl_crystal.colour 'pale yellow' _exptl_crystal.density_diffrn 1.113 _exptl_crystal.density_Matthews 1.01 _exptl_crystal.density_meas 1.11 _exptl_crystal.density_meas_temp 294.5 _exptl_crystal.density_method 'neutral buoyancy' _exptl_crystal.density_percent_sol 0.15 # P = 1 - (1.23*N*MMass) / V _exptl_crystal.description 'hexagonal rod, uncut' _exptl_crystal.F_000 202 _exptl_crystal.preparation ; hanging drop, crystal soaked in 10% ethylene glycol for 10 h, then placed in nylon loop at data collection time ; _exptl_crystal.size_max 0.30 _exptl_crystal.size_mid 0.20 _exptl_crystal.size_min 0.05 _exptl_crystal.size_rad 0.025 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - using separate items to define upper and lower limits for a value. ; ; _exptl_crystal.density_meas_gt 2.5 _exptl_crystal.density_meas_lt 5.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 3 - here the density was measured at some unspecified temperature below room temperature. ; ; _exptl_crystal.density_meas_temp_lt 300 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal.colour _item_description.description ; The colour of the crystal. ; _item.name '_exptl_crystal.colour' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_colour' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case 'dark green' save_ save__exptl_crystal.density_diffrn _item_description.description ; Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). ; _item.name '_exptl_crystal.density_diffrn' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_diffrn' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__exptl_crystal.density_Matthews _item_description.description ; The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. ; _item.name '_exptl_crystal.density_Matthews' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float save_ #save__exptl_crystal.density_meas # _item_description.description #; Density values measured using standard chemical and physical # methods. The units are megagrams per cubic metre (grams per # cubic centimetre). #; # _item.name '_exptl_crystal.density_meas' # _item.category_id exptl_crystal # _item.mandatory_code no # _item_aliases.alias_name '_exptl_crystal_density_meas' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_type.code float # save_ # #save__exptl_crystal.density_meas_temp # _item_description.description #; The temperature in kelvins at which _exptl_crystal.density_meas # was determined. #; # _item.name '_exptl_crystal.density_meas_temp' # _item.category_id exptl_crystal # _item.mandatory_code no # _item_aliases.alias_name '_exptl_crystal_density_meas_temp' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # loop_ # _item_range.maximum # _item_range.minimum . 0.0 # 0.0 0.0 # _item_type.code float # _item_units.code kelvins # save_ save__exptl_crystal.density_method _item_description.description ; The method used to measure _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_method' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_density_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__exptl_crystal.density_percent_sol _item_description.description ; Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule ; _item.name '_exptl_crystal.density_percent_sol' _item.category_id exptl_crystal _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__exptl_crystal.description _item_description.description ; A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. ; _item.name '_exptl_crystal.description' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_description' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__exptl_crystal.F_000 _item_description.description ; The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 degree f~i~ = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell ; _item.name '_exptl_crystal.F_000' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_F_000' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__exptl_crystal.id _item_description.description ; The value of _exptl_crystal.id must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_exptl_crystal.id' exptl_crystal yes '_exptl_crystal_face.crystal_id' exptl_crystal_face yes '_exptl_crystal_grow.crystal_id' exptl_crystal_grow yes '_exptl_crystal_grow_comp.crystal_id' exptl_crystal_grow_comp yes '_diffrn.crystal_id' diffrn yes '_refln.crystal_id' refln yes _item_aliases.alias_name '_exptl_crystal_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn.crystal_id' '_exptl_crystal.id' '_exptl_crystal_grow.crystal_id' '_exptl_crystal.id' '_exptl_crystal_face.crystal_id' '_exptl_crystal.id' '_exptl_crystal_grow_comp.crystal_id' '_exptl_crystal.id' '_refln.crystal_id' '_exptl_crystal.id' _item_type.code code save_ save__exptl_crystal.preparation _item_description.description ; Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. ; _item.name '_exptl_crystal.preparation' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_preparation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'mounted in an argon-filled quartz capillary' save_ save__exptl_crystal.size_max _item_description.description ; The maximum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_max' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__exptl_crystal.size_mid _item_description.description ; The medial dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_mid' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_mid' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__exptl_crystal.size_min _item_description.description ; The minimum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_min' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ save__exptl_crystal.size_rad _item_description.description ; The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment. ; _item.name '_exptl_crystal.size_rad' _item.category_id exptl_crystal _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_size_rad' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ ######################## ## EXPTL_CRYSTAL_FACE ## ######################## save_exptl_crystal_face _category.description ; Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. ; _category.id exptl_crystal_face _category.mandatory_code no loop_ _category_key.name '_exptl_crystal_face.crystal_id' '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_k' '_exptl_crystal_face.index_l' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4 for the 100 face of crystal xstl1. ; ; _exptl_crystal_face.crystal_id xstl1 _exptl_crystal_face.index_h 1 _exptl_crystal_face.index_k 0 _exptl_crystal_face.index_l 0 _exptl_crystal_face.diffr_chi 42.56 _exptl_crystal_face.diffr_kappa 30.23 _exptl_crystal_face.diffr_phi -125.56 _exptl_crystal_face.diffr_psi -0.34 _exptl_crystal_face.perp_dist 0.025 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal_face.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_exptl_crystal_face.crystal_id' _item.mandatory_code yes save_ save__exptl_crystal_face.diffr_chi _item_description.description ; The chi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_chi' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_chi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.diffr_kappa _item_description.description ; The kappa diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_kappa' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_kappa' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.diffr_phi _item_description.description ; The phi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_phi' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_phi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.diffr_psi _item_description.description ; The psi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.diffr_psi' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_diffr_psi' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__exptl_crystal_face.index_h _item_description.description ; Miller index h of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_h' _item.category_id exptl_crystal_face _item.mandatory_code yes _item_aliases.alias_name '_exptl_crystal_face_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_k' '_exptl_crystal_face.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__exptl_crystal_face.index_k _item_description.description ; Miller index k of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_k' _item.category_id exptl_crystal_face _item.mandatory_code yes _item_aliases.alias_name '_exptl_crystal_face_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__exptl_crystal_face.index_l _item_description.description ; Miller index l of the crystal face associated with the value _exptl_crystal_face.perp_dist. ; _item.name '_exptl_crystal_face.index_l' _item.category_id exptl_crystal_face _item.mandatory_code yes _item_aliases.alias_name '_exptl_crystal_face_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_exptl_crystal_face.index_h' '_exptl_crystal_face.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__exptl_crystal_face.perp_dist _item_description.description ; The perpendicular distance in millimetres from the face to the centre of rotation of the crystal. ; _item.name '_exptl_crystal_face.perp_dist' _item.category_id exptl_crystal_face _item.mandatory_code no _item_aliases.alias_name '_exptl_crystal_face_perp_dist' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code millimetres save_ ######################## ## EXPTL_CRYSTAL_GROW ## ######################## save_exptl_crystal_grow _category.description ; Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. ; _category.id exptl_crystal_grow _category.mandatory_code no _category_key.name '_exptl_crystal_grow.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'hanging drop' _exptl_crystal_grow.apparatus 'Linbro plates' _exptl_crystal_grow.atmosphere 'room air' _exptl_crystal_grow.pH 4.7 _exptl_crystal_grow.temp 18(3) _exptl_crystal_grow.time 'approximately 2 days' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal_grow.apparatus _item_description.description ; The physical apparatus in which the crystal was grown. ; _item.name '_exptl_crystal_grow.apparatus' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Linbro plate' 'sandwich box' 'ACA plates' save_ save__exptl_crystal_grow.atmosphere _item_description.description ; The nature of the gas or gas mixture in which the crystal was grown. ; _item.name '_exptl_crystal_grow.atmosphere' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'room air' 'nitrogen' 'argon' save_ save__exptl_crystal_grow.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_exptl_crystal_grow.crystal_id' _item.mandatory_code yes save_ save__exptl_crystal_grow.details _item_description.description ; A description of special aspects of the crystal growth. ; _item.name '_exptl_crystal_grow.details' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. ; ; Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. ; ; The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. ; save_ save__exptl_crystal_grow.method _item_description.description ; The method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'batch precipitation' 'batch dialysis' 'hanging drop vapor diffusion' 'sitting drop vapor diffusion' save_ save__exptl_crystal_grow.method_ref _item_description.description ; A literature reference that describes the method used to grow the crystals. ; _item.name '_exptl_crystal_grow.method_ref' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'McPherson et al., 1988' save_ save__exptl_crystal_grow.pH _item_description.description ; The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details. ; _item.name '_exptl_crystal_grow.pH' _item.category_id exptl_crystal_grow _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float loop_ _item_examples.case 7.4 7.6 4.3 save_ save__exptl_crystal_grow.pressure _item_description.description ; The ambient pressure in kilopascals at which the crystal was grown. ; _item.name '_exptl_crystal_grow.pressure' _item.category_id exptl_crystal_grow _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_exptl_crystal_grow.pressure_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kilopascals save_ save__exptl_crystal_grow.pressure_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _exptl_crystal_grow.pressure. ; _item.name '_exptl_crystal_grow.pressure_esd' _item.category_id exptl_crystal_grow _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_exptl_crystal_grow.pressure' _item_related.function_code associated_value _item_type.code float _item_units.code kilopascals save_ save__exptl_crystal_grow.seeding _item_description.description ; A description of the protocol used for seeding the crystal growth. ; _item.name '_exptl_crystal_grow.seeding' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'macroseeding' ; Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. ; save_ save__exptl_crystal_grow.seeding_ref _item_description.description ; A literature reference that describes the protocol used to seed the crystal. ; _item.name '_exptl_crystal_grow.seeding_ref' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text _item_examples.case 'Stura et al., 1989' save_ save__exptl_crystal_grow.temp _item_description.description ; The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details. ; _item.name '_exptl_crystal_grow.temp' _item.category_id exptl_crystal_grow _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_exptl_crystal_grow.temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvins save_ save__exptl_crystal_grow.temp_details _item_description.description ; A description of special aspects of temperature control during crystal growth. ; _item.name '_exptl_crystal_grow.temp_details' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text save_ save__exptl_crystal_grow.temp_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _exptl_crystal_grow.temp. ; _item.name '_exptl_crystal_grow.temp_esd' _item.category_id exptl_crystal_grow _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_exptl_crystal_grow.temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvins save_ save__exptl_crystal_grow.time _item_description.description ; The approximate time that the crystal took to grow to the size used for data collection. ; _item.name '_exptl_crystal_grow.time' _item.category_id exptl_crystal_grow _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'overnight' '2-4 days' '6 months' save_ ############################# ## EXPTL_CRYSTAL_GROW_COMP ## ############################# save_exptl_crystal_grow_comp _category.description ; Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in _exptl_crystal_grow_comp.details using the solutions described in EXPTL_CRYSTAL_GROW_COMP. ; _category.id exptl_crystal_grow_comp _category.mandatory_code no loop_ _category_key.name '_exptl_crystal_grow_comp.id' '_exptl_crystal_grow_comp.crystal_id' loop_ _category_group.id 'inclusive_group' 'exptl_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'HIV-1 protease' '0.002 ml' '6 mg/ml' ; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide ; 1 2 2 'NaCl' '0.200 ml' '4 M' 'in 3 mM NaAzide' 1 3 2 'Acetic Acid' '0.047 ml' '100 mM' 'in 3 mM NaAzide' 1 4 2 'Na Acetate' '0.053 ml' '100 mM' ; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. ; 1 5 2 'water' '0.700 ml' 'neat' 'in 3 mM NaAzide' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__exptl_crystal_grow_comp.conc _item_description.description ; The concentration of the solution component. ; _item.name '_exptl_crystal_grow_comp.conc' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '200 \ml' '0.1 ml' save_ save__exptl_crystal_grow_comp.details _item_description.description ; A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. ; _item.name '_exptl_crystal_grow_comp.details' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'in 3 mM NaAzide' ; The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide ; ; in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. ; save_ save__exptl_crystal_grow_comp.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_exptl_crystal_grow_comp.crystal_id' _item.mandatory_code yes save_ save__exptl_crystal_grow_comp.id _item_description.description ; The value of _exptl_crystal_grow_comp.id must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_exptl_crystal_grow_comp.id' _item.category_id exptl_crystal_grow_comp _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '1' 'A' 'protein in buffer' save_ save__exptl_crystal_grow_comp.name _item_description.description ; A common name for the component of the solution. ; _item.name '_exptl_crystal_grow_comp.name' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'protein in buffer' 'acetic acid' save_ save__exptl_crystal_grow_comp.sol_id _item_description.description ; An identifier for the solution to which the given solution component belongs. ; _item.name '_exptl_crystal_grow_comp.sol_id' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '1' 'well solution' 'solution A' save_ save__exptl_crystal_grow_comp.volume _item_description.description ; The volume of the solution component. ; _item.name '_exptl_crystal_grow_comp.volume' _item.category_id exptl_crystal_grow_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case '200 \ml' '0.1 ml' save_ ########## ## GEOM ## ########## save_geom _category.description ; Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag. ; _category.id geom _category.mandatory_code no _category_key.name '_geom.entry_id' loop_ _category_group.id 'inclusive_group' 'geom_group' save_ save__geom.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_geom.entry_id' _item.mandatory_code yes save_ save__geom.details _item_description.description ; A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes. ; _item.name '_geom.details' _item.category_id geom _item.mandatory_code no _item_aliases.alias_name '_geom_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ################ ## GEOM_ANGLE ## ################ save_geom_angle _category.description ; Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_angle _category.mandatory_code no loop_ _category_key.name '_geom_angle.atom_site_id_1' '_geom_angle.atom_site_id_2' '_geom_angle.atom_site_id_3' '_geom_angle.site_symmetry_1' '_geom_angle.site_symmetry_2' '_geom_angle.site_symmetry_3' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _geom_angle.atom_site_id_1 _geom_angle.atom_site_id_2 _geom_angle.atom_site_id_3 _geom_angle.value _geom_angle.value_esd _geom_angle.site_symmetry_1 _geom_angle.site_symmetry_2 _geom_angle.site_symmetry_3 _geom_angle.publ_flag C2 O1 C5 111.6 0.2 1_555 1_555 1_555 yes O1 C2 C3 110.9 0.2 1_555 1_555 1_555 yes O1 C2 O21 122.2 0.3 1_555 1_555 1_555 yes C3 C2 O21 127.0 0.3 1_555 1_555 1_555 yes C2 C3 N4 101.3 0.2 1_555 1_555 1_555 yes C2 C3 C31 111.3 0.2 1_555 1_555 1_555 yes C2 C3 H3 107 1 1_555 1_555 1_555 no N4 C3 C31 116.7 0.2 1_555 1_555 1_555 yes # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_angle.atom_site_id_1 _item_description.description ; The identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_angle.atom_site_id_2' '_geom_angle.atom_site_id_3' save_ save__geom_angle.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_id_2 _item_description.description ; The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_angle.atom_site_id_1' '_geom_angle.atom_site_id_3' save_ save__geom_angle.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_id_3 _item_description.description ; The identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_id_3' _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_atom_site_label_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_angle.atom_site_id_1' '_geom_angle.atom_site_id_2' save_ save__geom_angle.atom_site_label_alt_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_alt_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_atom_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_atom_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_comp_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_comp_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_seq_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_seq_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_label_asym_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_label_asym_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_atom_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_atom_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_asym_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_asym_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_comp_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_comp_id_3' _item.mandatory_code no save_ save__geom_angle.atom_site_auth_seq_id_3 _item_description.description ; An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_angle.atom_site_auth_seq_id_3' _item.mandatory_code no save_ save__geom_angle.publ_flag _item_description.description ; This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. ; _item.name '_geom_angle.publ_flag' _item.category_id geom_angle _item.mandatory_code no _item_aliases.alias_name '_geom_angle_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"' save_ save__geom_angle.site_symmetry_1 _item_description.description ; The symmetry code of the first of the three atom sites that define the angle. ; _item.name '_geom_angle.site_symmetry_1' _item.category_id geom_angle _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_angle.site_symmetry_2 _item_description.description ; The symmetry code of the second of the three atom sites that define the angle. ; _item.name '_geom_angle.site_symmetry_2' _item.category_id geom_angle _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_angle.site_symmetry_3 _item_description.description ; The symmetry code of the third of the three atom sites that define the angle. ; _item.name '_geom_angle.site_symmetry_3' _item.category_id geom_angle _item.mandatory_code yes _item_aliases.alias_name '_geom_angle_site_symmetry_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_angle.value _item_description.description ; Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and _geom_angle.atom_site_id_3. ; _item.name '_geom_angle.value' _item.category_id geom_angle _item.mandatory_code no _item_aliases.alias_name '_geom_angle' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_geom_angle.value_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__geom_angle.value_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_angle.value. ; _item.name '_geom_angle.value_esd' _item.category_id geom_angle _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_angle.value' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ ############### ## GEOM_BOND ## ############### save_geom_bond _category.description ; Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_bond _category.mandatory_code no loop_ _category_key.name '_geom_bond.atom_site_id_1' '_geom_bond.atom_site_id_2' '_geom_bond.site_symmetry_1' '_geom_bond.site_symmetry_2' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _geom_bond.atom_site_id_1 _geom_bond.atom_site_id_2 _geom_bond.dist _geom_bond.dist_esd _geom_bond.site_symmetry_1 _geom_bond.site_symmetry_2 _geom_bond.publ_flag O1 C2 1.342 0.004 1_555 1_555 yes O1 C5 1.439 0.003 1_555 1_555 yes C2 C3 1.512 0.004 1_555 1_555 yes C2 O21 1.199 0.004 1_555 1_555 yes C3 N4 1.465 0.003 1_555 1_555 yes C3 C31 1.537 0.004 1_555 1_555 yes C3 H3 1.00 0.03 1_555 1_555 no N4 C5 1.472 0.003 1_555 1_555 yes # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_bond.atom_site_id_1 _item_description.description ; The identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_bond.atom_site_id_2' save_ save__geom_bond.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_id_2 _item_description.description ; The identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_bond.atom_site_id_1' save_ save__geom_bond.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_bond.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_bond.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_bond.dist _item_description.description ; The intramolecular bond distance in angstroms. ; _item.name '_geom_bond.dist' _item.category_id geom_bond _item.mandatory_code no _item_aliases.alias_name '_geom_bond_distance' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_bond.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_bond.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_bond.dist. ; _item.name '_geom_bond.dist_esd' _item.category_id geom_bond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_bond.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_bond.publ_flag _item_description.description ; This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances. ; _item.name '_geom_bond.publ_flag' _item.category_id geom_bond _item.mandatory_code no _item_aliases.alias_name '_geom_bond_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"' save_ save__geom_bond.site_symmetry_1 _item_description.description ; The symmetry code of the first of the two atom sites that define the bond. ; _item.name '_geom_bond.site_symmetry_1' _item.category_id geom_bond _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_bond.site_symmetry_2 _item_description.description ; The symmetry code of the second of the two atom sites that define the bond. ; _item.name '_geom_bond.site_symmetry_2' _item.category_id geom_bond _item.mandatory_code yes _item_aliases.alias_name '_geom_bond_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ################## ## GEOM_CONTACT ## ################## save_geom_contact _category.description ; Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_contact _category.mandatory_code no loop_ _category_key.name '_geom_contact.atom_site_id_1' '_geom_contact.atom_site_id_2' '_geom_contact.site_symmetry_1' '_geom_contact.site_symmetry_2' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. ; ; loop_ _geom_contact.atom_site_id_1 _geom_contact.atom_site_id_2 _geom_contact.dist _geom_contact.dist_esd _geom_contact.site_symmetry_1 _geom_contact.site_symmetry_2 _geom_contact.publ_flag O(1) O(2) 2.735 0.003 . . yes H(O1) O(2) 1.82 . . . no ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_contact.atom_site_id_1 _item_description.description ; The identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_contact.atom_site_id_2' save_ save__geom_contact.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_id_2 _item_description.description ; The identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_dependent.dependent_name '_geom_contact.atom_site_id_1' save_ save__geom_contact.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_contact.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_contact.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_contact.dist _item_description.description ; The interatomic contact distance in angstroms. ; _item.name '_geom_contact.dist' _item.category_id geom_contact _item.mandatory_code no _item_aliases.alias_name '_geom_contact_distance' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_contact.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_contact.dist_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_contact.dist. ; _item.name '_geom_contact.dist_esd' _item.category_id geom_contact _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_contact.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_contact.publ_flag _item_description.description ; This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances. ; _item.name '_geom_contact.publ_flag' _item.category_id geom_contact _item.mandatory_code no _item_aliases.alias_name '_geom_contact_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include distance in special list' n 'abbreviation for "no"' yes 'do include distance in special list' y 'abbreviation for "yes"' save_ save__geom_contact.site_symmetry_1 _item_description.description ; The symmetry code of the first of the two atom sites that define the contact. ; _item.name '_geom_contact.site_symmetry_1' _item.category_id geom_contact _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_contact.site_symmetry_2 _item_description.description ; The symmetry code of the second of the two atom sites that define the contact. ; _item.name '_geom_contact.site_symmetry_2' _item.category_id geom_contact _item.mandatory_code yes _item_aliases.alias_name '_geom_contact_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ################ ## GEOM_HBOND ## ################ save_geom_hbond _category.description ; Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data. ; _category.id geom_hbond _category.mandatory_code no loop_ _category_key.name '_geom_hbond.atom_site_id_A' '_geom_hbond.atom_site_id_D' '_geom_hbond.atom_site_id_H' '_geom_hbond.site_symmetry_A' '_geom_hbond.site_symmetry_D' '_geom_hbond.site_symmetry_H' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. ; ; loop_ _geom_hbond.atom_site_id_D _geom_hbond.atom_site_id_H _geom_hbond.atom_site_id_A _geom_hbond.dist_DH _geom_hbond.dist_HA _geom_hbond.dist_DA _geom_hbond.angle_DHA _geom_hbond.publ_flag N6 HN6 OW 0.888 1.921 2.801 169.6 yes OW HO2 O7 0.917 1.923 2.793 153.5 yes OW HO1 N10 0.894 1.886 2.842 179.7 yes ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_hbond.angle_DHA _item_description.description ; The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond. ; _item.name '_geom_hbond.angle_DHA' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_angle_DHA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.angle_DHA_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.angle_DHA_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_hbond.angle_DHA. ; _item.name '_geom_hbond.angle_DHA_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.angle_DHA' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.atom_site_id_A _item_description.description ; The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_id_A' _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_atom_site_label_A' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_hbond.atom_site_id_D' '_geom_hbond.atom_site_id_H' save_ save__geom_hbond.atom_site_label_alt_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_alt_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_asym_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_asym_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_atom_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_atom_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_comp_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_comp_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_seq_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_seq_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_id_D _item_description.description ; The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_id_D' _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_atom_site_label_D' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_hbond.atom_site_id_A' '_geom_hbond.atom_site_id_H' save_ save__geom_hbond.atom_site_label_alt_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_alt_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_asym_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_asym_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_atom_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_atom_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_comp_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_comp_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_seq_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_seq_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_id_H _item_description.description ; The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_id_H' _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_atom_site_label_H' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_hbond.atom_site_id_A' '_geom_hbond.atom_site_id_D' save_ save__geom_hbond.atom_site_label_alt_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_alt_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_asym_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_asym_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_atom_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_atom_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_comp_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_comp_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_label_seq_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_label_seq_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_asym_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_asym_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_atom_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_atom_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_comp_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_comp_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_seq_id_A _item_description.description ; An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_seq_id_A' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_asym_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_asym_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_atom_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_atom_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_comp_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_comp_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_seq_id_D _item_description.description ; An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_seq_id_D' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_asym_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_asym_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_atom_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_atom_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_comp_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_comp_id_H' _item.mandatory_code no save_ save__geom_hbond.atom_site_auth_seq_id_H _item_description.description ; An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_hbond.atom_site_auth_seq_id_H' _item.mandatory_code no save_ save__geom_hbond.dist_DA _item_description.description ; The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond. ; _item.name '_geom_hbond.dist_DA' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_distance_DA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.dist_DA_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.dist_DA_esd _item_description.description ; The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_DA. ; _item.name '_geom_hbond.dist_DA_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.dist_DH' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.dist_DH _item_description.description ; The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond. ; _item.name '_geom_hbond.dist_DH' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_distance_DH' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.dist_DH_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.dist_DH_esd _item_description.description ; The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_DH. ; _item.name '_geom_hbond.dist_DH_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.dist_DH' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.dist_HA _item_description.description ; The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond. ; _item.name '_geom_hbond.dist_HA' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_distance_HA' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_geom_hbond.dist_HA_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__geom_hbond.dist_HA_esd _item_description.description ; The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_HA. ; _item.name '_geom_hbond.dist_HA_esd' _item.category_id geom_hbond _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_hbond.dist_HA' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__geom_hbond.publ_flag _item_description.description ; This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. ; _item.name '_geom_hbond.publ_flag' _item.category_id geom_hbond _item.mandatory_code no _item_aliases.alias_name '_geom_hbond_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include bond in special list' n 'abbreviation for "no"' yes 'do include bond in special list' y 'abbreviation for "yes"' save_ save__geom_hbond.site_symmetry_A _item_description.description ; The symmetry code of the acceptor-atom site that defines the hydrogen bond. ; _item.name '_geom_hbond.site_symmetry_A' _item.category_id geom_hbond _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_site_symmetry_A' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_hbond.site_symmetry_D _item_description.description ; The symmetry code of the donor-atom site that defines the hydrogen bond. ; _item.name '_geom_hbond.site_symmetry_D' _item.category_id geom_hbond _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_site_symmetry_D' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_hbond.site_symmetry_H _item_description.description ; The symmetry code of the hydrogen-atom site that defines the hydrogen bond. ; _item.name '_geom_hbond.site_symmetry_H' _item.category_id geom_hbond _item.mandatory_code yes _item_aliases.alias_name '_geom_hbond_site_symmetry_H' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ################## ## GEOM_TORSION ## ################## save_geom_torsion _category.description ; Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction _geom_torsion.atom_site_id_2 to _geom_torsion.atom_site_id_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. ; _category.id geom_torsion _category.mandatory_code no loop_ _category_key.name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_3' '_geom_torsion.atom_site_id_4' '_geom_torsion.site_symmetry_1' '_geom_torsion.site_symmetry_2' '_geom_torsion.site_symmetry_3' '_geom_torsion.site_symmetry_4' loop_ _category_group.id 'inclusive_group' 'geom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. ; ; loop_ _geom_torsion.atom_site_id_1 _geom_torsion.atom_site_id_2 _geom_torsion.atom_site_id_3 _geom_torsion.atom_site_id_4 _geom_torsion.value _geom_torsion.site_symmetry_1 _geom_torsion.site_symmetry_2 _geom_torsion.site_symmetry_3 _geom_torsion.site_symmetry_4 _geom_torsion.publ_flag C(9) O(2) C(7) C(2) 71.8 . . . . yes C(7) O(2) C(9) C(10) -168.0 . . . 2_666 yes C(10) O(3) C(8) C(6) -167.7 . . . . yes C(8) O(3) C(10) C(9) -69.7 . . . 2_666 yes O(1) C(1) C(2) C(3) -179.5 . . . . no O(1) C(1) C(2) C(7) -0.6 . . . . no ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__geom_torsion.atom_site_id_1 _item_description.description ; The identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_1' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_3' '_geom_torsion.atom_site_id_4' save_ save__geom_torsion.atom_site_label_alt_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_id_2 _item_description.description ; The identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_2' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_3' '_geom_torsion.atom_site_id_4' save_ save__geom_torsion.atom_site_label_alt_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_id_3 _item_description.description ; The identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_3' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_4' save_ save__geom_torsion.atom_site_label_alt_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_id_4 _item_description.description ; The identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_id_4' _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_atom_site_label_4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_geom_torsion.atom_site_id_1' '_geom_torsion.atom_site_id_2' '_geom_torsion.atom_site_id_3' save_ save__geom_torsion.atom_site_label_alt_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_alt_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_atom_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_atom_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_comp_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_comp_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_seq_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_seq_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_label_asym_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_label_asym_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_1 _item_description.description ; An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_1' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_2 _item_description.description ; An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_2' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_3 _item_description.description ; An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_3' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_atom_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_atom_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_asym_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_asym_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_comp_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_comp_id_4' _item.mandatory_code no save_ save__geom_torsion.atom_site_auth_seq_id_4 _item_description.description ; An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_geom_torsion.atom_site_auth_seq_id_4' _item.mandatory_code no save_ save__geom_torsion.publ_flag _item_description.description ; This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. ; _item.name '_geom_torsion.publ_flag' _item.category_id geom_torsion _item.mandatory_code no _item_aliases.alias_name '_geom_torsion_publ_flag' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'do not include angle in special list' n 'abbreviation for "no"' yes 'do include angle in special list' y 'abbreviation for "yes"' save_ save__geom_torsion.site_symmetry_1 _item_description.description ; The symmetry code of the first of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_1' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_1' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.site_symmetry_2 _item_description.description ; The symmetry code of the second of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_2' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_2' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.site_symmetry_3 _item_description.description ; The symmetry code of the third of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_3' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_3' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.site_symmetry_4 _item_description.description ; The symmetry code of the fourth of the four atom sites that define the torsion angle. ; _item.name '_geom_torsion.site_symmetry_4' _item.category_id geom_torsion _item.mandatory_code yes _item_aliases.alias_name '_geom_torsion_site_symmetry_4' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__geom_torsion.value _item_description.description ; The value of the torsion angle in degrees. ; _item.name '_geom_torsion.value' _item.category_id geom_torsion _item.mandatory_code no _item_aliases.alias_name '_geom_torsion' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_geom_torsion.value_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__geom_torsion.value_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _geom_torsion.value. ; _item.name '_geom_torsion.value_esd' _item.category_id geom_torsion _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_geom_torsion.value' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ ############# ## JOURNAL ## ############# save_journal _category.description ; Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only. ; _category.id journal _category.mandatory_code no _category_key.name '_journal.entry_id' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. ; ; _journal.entry_id 'TOZ' _journal.date_recd_electronic 1991-04-15 _journal.date_from_coeditor 1991-04-18 _journal.date_accepted 1991-04-18 _journal.date_printers_first 1991-08-07 _journal.date_proofs_out 1991-08-07 _journal.coeditor_code HL0007 _journal.techeditor_code C910963 _journal.coden_ASTM ACSCEE _journal.name_full 'Acta Crystallographica Section C' _journal.year 1991 _journal.volume 47 _journal.issue NOV91 _journal.page_first 2276 _journal.page_last 2277 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__journal.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_journal.entry_id' _item.mandatory_code yes save_ save__journal.coden_ASTM _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_ASTM' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coden_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coden_Cambridge _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coden_Cambridge' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coden_Cambridge' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_address _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_address' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.coeditor_code _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_code' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_email _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_email' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_fax _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_fax' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_name _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_name' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.coeditor_notes _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_notes' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_notes' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.coeditor_phone _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.coeditor_phone' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_coeditor_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.data_validation_number _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.data_validation_number' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_data_validation_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__journal.date_accepted _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_accepted' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_accepted' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_from_coeditor _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_from_coeditor' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_from_coeditor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_to_coeditor _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_to_coeditor' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_to_coeditor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_printers_final _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_final' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_final' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_printers_first _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_printers_first' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_printers_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_proofs_in _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_in' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_in' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_proofs_out _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_proofs_out' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_proofs_out' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_recd_copyright _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_copyright' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_copyright' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_recd_electronic _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_electronic' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_electronic' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.date_recd_hard_copy _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.date_recd_hard_copy' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_date_recd_hard_copy' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code yyyy-mm-dd save_ save__journal.issue _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.issue' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_issue' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.language _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.language' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_language' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.name_full _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.name_full' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_name_full' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.page_first _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_first' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_page_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.page_last _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.page_last' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_page_last' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.paper_category _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.paper_category' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_paper_category' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.suppl_publ_number _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_number' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.suppl_publ_pages _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.suppl_publ_pages' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_suppl_publ_pages' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_address _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_address' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.techeditor_code _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_code' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_email _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_email' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_fax _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_fax' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_name _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_name' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.techeditor_notes _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_notes' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_notes' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__journal.techeditor_phone _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.techeditor_phone' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_techeditor_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.volume _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.volume' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal.year _item_description.description ; Journal data items are defined by the journal staff. ; _item.name '_journal.year' _item.category_id journal _item.mandatory_code no _item_aliases.alias_name '_journal_year' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ################### ## JOURNAL_INDEX ## ################### save_journal_index _category.description ; Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items. ; _category.id journal_index _category.mandatory_code no loop_ _category_key.name '_journal_index.type' '_journal_index.term' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. ; ; loop_ _journal_index.type _journal_index.term _journal_index.subterm O C16H19NO4 . S alkaloids (-)-norcocaine S (-)-norcocaine . S ; [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate ; . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__journal_index.subterm _item_description.description ; Journal index data items are defined by the journal staff. ; _item.name '_journal_index.subterm' _item.category_id journal_index _item.mandatory_code no _item_aliases.alias_name '_journal_index_subterm' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal_index.term _item_description.description ; Journal index data items are defined by the journal staff. ; _item.name '_journal_index.term' _item.category_id journal_index _item.mandatory_code no _item_aliases.alias_name '_journal_index_term' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__journal_index.type _item_description.description ; Journal index data items are defined by the journal staff. ; _item.name '_journal_index.type' _item.category_id journal_index _item.mandatory_code no _item_aliases.alias_name '_journal_index_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ ############# ## PHASING ## ############# save_phasing _category.description ; Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories. ; _category.id phasing _category.mandatory_code no _category_key.name '_phasing.method' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _phasing.method 'mir' 'averaging' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing.method _item_description.description ; A listing of the method or methods used to phase this structure. ; _item.name '_phasing.method' _item.category_id phasing _item.mandatory_code yes _item_type.code ucode loop_ _item_examples.case _item_examples.detail abinitio ; phasing by ab initio methods ; averaging ; phase improvement by averaging over multiple images of the structure ; dm ; phasing by direct methods ; isas ; phasing by iterative single-wavelength anomalous scattering ; isir ; phasing by iterative single-wavelength isomorphous replacement ; isomorphous ; phasing beginning with phases calculated from an isomorphous structure ; mad ; phasing by multiple-wavelength anomalous dispersion ; mir ; phasing by multiple isomorphous replacement ; miras ; phasing by multiple isomorphous replacement with anomalous scattering ; mr ; phasing by molecular replacement ; sir ; phasing by single isomorphous replacement ; siras ; phasing by single isomorphous replacement with anomalous scattering ; save_ ####################### ## PHASING_AVERAGING ## ####################### save_phasing_averaging _category.description ; Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved. ; _category.id phasing_averaging _category.mandatory_code no _category_key.name '_phasing_averaging.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; _phasing_averaging.entry_id 'EXAMHYPO' _phasing_averaging.method ; Iterative threefold averaging alternating with phase extensions by 0.5 reciprocal lattice units per cycle. ; _phasing_averaging.details ; The position of the threefold axis was redetermined every five cycles. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_averaging.details _item_description.description ; A description of special aspects of the averaging process. ; _item.name '_phasing_averaging.details' _item.category_id phasing_averaging _item.mandatory_code no _item_type.code text save_ save__phasing_averaging.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_averaging.entry_id' _item.mandatory_code yes save_ save__phasing_averaging.method _item_description.description ; A description of the phase-averaging phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the phase-averaging program. ; _item.name '_phasing_averaging.method' _item.category_id phasing_averaging _item.mandatory_code no _item_type.code text save_ ######################### ## PHASING_ISOMORPHOUS ## ######################### save_phasing_isomorphous _category.description ; Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases. ; _category.id phasing_isomorphous _category.mandatory_code no _category_key.name '_phasing_isomorphous.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV. ; ; _phasing_isomorphous.parent 'PDB entry 5HVP' _phasing_isomorphous.details ; The inhibitor and all solvent atoms were removed from the parent structure before beginning refinement. All static disorder present in the parent structure was also removed. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_isomorphous.details _item_description.description ; A description of special aspects of the isomorphous phasing. ; _item.name '_phasing_isomorphous.details' _item.category_id phasing_isomorphous _item.mandatory_code no _item_type.code text _item_examples.case ; Residues 13-18 were eliminated from the starting model as it was anticipated that binding of the inhibitor would cause a structural rearrangement in this part of the structure. ; save_ save__phasing_isomorphous.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_isomorphous.entry_id' _item.mandatory_code yes save_ save__phasing_isomorphous.method _item_description.description ; A description of the isomorphous-phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the isomorphous phasing program. ; _item.name '_phasing_isomorphous.method' _item.category_id phasing_isomorphous _item.mandatory_code no _item_type.code text _item_examples.case ; Iterative threefold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle. ; save_ save__phasing_isomorphous.parent _item_description.description ; Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g. a mutant that crystallizes in the same space group as the wild-type protein.) ; _item.name '_phasing_isomorphous.parent' _item.category_id phasing_isomorphous _item.mandatory_code no _item_type.code text save_ ################# ## PHASING_MAD ## ################# save_phasing_MAD _category.description ; Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved. ; _category.id phasing_MAD _category.mandatory_code no _category_key.name '_phasing_MAD.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; _phasing_MAD.entry_id 'NCAD' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD.details _item_description.description ; A description of special aspects of the MAD phasing. ; _item.name '_phasing_MAD.details' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code text save_ save__phasing_MAD.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_MAD.entry_id' _item.mandatory_code yes save_ save__phasing_MAD.method _item_description.description ; A description of the MAD phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program. ; _item.name '_phasing_MAD.method' _item.category_id phasing_MAD _item.mandatory_code no _item_type.code text save_ ####################### ## PHASING_MAD_CLUST ## ####################### save_phasing_MAD_clust _category.description ; Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases. ; _category.id phasing_MAD_clust _category.mandatory_code no loop_ _category_key.name '_phasing_MAD_clust.expt_id' '_phasing_MAD_clust.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_clust.id _phasing_MAD_clust.expt_id _phasing_MAD_clust.number_set '4 wavelength' 1 4 '5 wavelength' 1 5 '5 wavelength' 2 5 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_clust.expt_id _item_description.description ; This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category. ; _item.name '_phasing_MAD_clust.expt_id' _item.mandatory_code yes save_ save__phasing_MAD_clust.id _item_description.description ; The value of _phasing_MAD_clust.id must, together with _phasing_MAD_clust.expt_id, uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MAD_clust.id' phasing_MAD_clust yes '_phasing_MAD_set.clust_id' phasing_MAD_set yes '_phasing_MAD_ratio.clust_id' phasing_MAD_ratio yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MAD_set.clust_id' '_phasing_MAD_clust.id' '_phasing_MAD_ratio.clust_id' '_phasing_MAD_clust.id' _item_type.code code save_ save__phasing_MAD_clust.number_set _item_description.description ; The number of data sets in this cluster of data sets. ; _item.name '_phasing_MAD_clust.number_set' _item.category_id phasing_MAD_clust _item.mandatory_code no _item_type.code int save_ ###################### ## PHASING_MAD_EXPT ## ###################### save_phasing_MAD_expt _category.description ; Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases. ; _category.id phasing_MAD_expt _category.mandatory_code no _category_key.name '_phasing_MAD_expt.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_expt.id _phasing_MAD_expt.number_clust _phasing_MAD_expt.R_normal_all _phasing_MAD_expt.R_normal_anom_scat _phasing_MAD_expt.delta_delta_phi _phasing_MAD_expt.delta_phi_sigma _phasing_MAD_expt.mean_fom 1 2 0.063 0.451 58.5 20.3 0.88 2 1 0.051 0.419 36.8 18.2 0.93 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_expt.delta_delta_phi _item_description.description ; The difference between two independent determinations of _phasing_MAD_expt.delta_phi. ; _item.name '_phasing_MAD_expt.delta_delta_phi' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_expt.delta_phi _item_description.description ; The phase difference between F~t~(h), the structure factor due to normal scattering from all atoms, and F~a~(h), the structure factor due to normal scattering from only the anomalous scatterers. ; _item.name '_phasing_MAD_expt.delta_phi' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float _item_related.related_name '_phasing_MAD_expt.delta_phi_sigma' _item_related.function_code associated_esd save_ save__phasing_MAD_expt.delta_phi_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MAD_expt.delta_phi. ; _item.name '_phasing_MAD_expt.delta_phi_sigma' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_related.related_name '_phasing_MAD_expt.delta_phi' _item_related.function_code associated_value _item_type.code float save_ save__phasing_MAD_expt.id _item_description.description ; The value of _phasing_MAD_expt.id must uniquely identify each record in the PHASING_MAD_EXPT list. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MAD_expt.id' phasing_MAD_expt yes '_phasing_MAD_clust.expt_id' phasing_MAD_clust yes '_phasing_MAD_set.expt_id' phasing_MAD_set yes '_phasing_MAD_ratio.expt_id' phasing_MAD_ratio yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MAD_clust.expt_id' '_phasing_MAD_expt.id' '_phasing_MAD_set.expt_id' '_phasing_MAD_expt.id' '_phasing_MAD_ratio.expt_id' '_phasing_MAD_expt.id' _item_type.code code save_ save__phasing_MAD_expt.mean_fom _item_description.description ; The mean figure of merit. ; _item.name '_phasing_MAD_expt.mean_fom' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_expt.number_clust _item_description.description ; The number of clusters of data sets in this phasing experiment. ; _item.name '_phasing_MAD_expt.number_clust' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code int save_ save__phasing_MAD_expt.R_normal_all _item_description.description ; Definition... ; _item.name '_phasing_MAD_expt.R_normal_all' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_expt.R_normal_anom_scat _item_description.description ; Definition... ; _item.name '_phasing_MAD_expt.R_normal_anom_scat' _item.category_id phasing_MAD_expt _item.mandatory_code no _item_type.code float save_ ####################### ## PHASING_MAD_RATIO ## ####################### save_phasing_MAD_ratio _category.description ; Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution. ; _category.id phasing_MAD_ratio _category.mandatory_code no loop_ _category_key.name '_phasing_MAD_ratio.clust_id' '_phasing_MAD_ratio.expt_id' '_phasing_MAD_ratio.wavelength_1' '_phasing_MAD_ratio.wavelength_2' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_ratio.expt_id _phasing_MAD_ratio.clust_id _phasing_MAD_ratio.wavelength_1 _phasing_MAD_ratio.wavelength_2 _phasing_MAD_ratio.d_res_low _phasing_MAD_ratio.d_res_high _phasing_MAD_ratio.ratio_two_wl _phasing_MAD_ratio.ratio_one_wl _phasing_MAD_ratio.ratio_one_wl_centric 1 '4 wavelength' 1.4013 1.4013 20.00 4.00 . 0.084 0.076 1 '4 wavelength' 1.4013 1.3857 20.00 4.00 0.067 . . 1 '4 wavelength' 1.4013 1.3852 20.00 4.00 0.051 . . 1 '4 wavelength' 1.4013 1.3847 20.00 4.00 0.044 . . 1 '4 wavelength' 1.3857 1.3857 20.00 4.00 . 0.110 0.049 1 '4 wavelength' 1.3857 1.3852 20.00 4.00 0.049 . . 1 '4 wavelength' 1.3857 1.3847 20.00 4.00 0.067 . . 1 '4 wavelength' 1.3852 1.3852 20.00 4.00 . 0.149 0.072 1 '4 wavelength' 1.3852 1.3847 20.00 4.00 0.039 . . 1 '4 wavelength' 1.3847 1.3847 20.00 4.00 . 0.102 0.071 1 '4 wavelength' 1.4013 1.4013 4.00 3.00 . 0.114 0.111 1 '4 wavelength' 1.4013 1.3857 4.00 3.00 0.089 . . 1 '4 wavelength' 1.4013 1.3852 4.00 3.00 0.086 . . 1 '4 wavelength' 1.4013 1.3847 4.00 3.00 0.077 . . 1 '4 wavelength' 1.3857 1.3857 4.00 3.00 . 0.140 0.127 1 '4 wavelength' 1.3857 1.3852 4.00 3.00 0.085 . . 1 '4 wavelength' 1.3857 1.3847 4.00 3.00 0.089 . . 1 '4 wavelength' 1.3852 1.3852 4.00 3.00 . 0.155 0.119 1 '4 wavelength' 1.3852 1.3847 4.00 3.00 0.082 . . 1 '4 wavelength' 1.3847 1.3847 4.00 3.00 . 0.124 0.120 1 '5 wavelength' 1.3857 1.3857 20.00 4.00 . 0.075 0.027 1 '5 wavelength' 1.3857 1.3852 20.00 4.00 0.041 . . 1 '5 wavelength' 1.3857 1.3847 20.00 4.00 0.060 . . 1 '5 wavelength' 1.3857 1.3784 20.00 4.00 0.057 . . 1 '5 wavelength' 1.3857 1.2862 20.00 4.00 0.072 . . 1 '5 wavelength' 1.3852 1.3852 20.00 4.00 . 0.105 0.032 1 '5 wavelength' 1.3852 1.3847 20.00 4.00 0.036 . . 1 '5 wavelength' 1.3852 1.3784 20.00 4.00 0.044 . . 1 '5 wavelength' 1.3852 1.2862 20.00 4.00 0.065 . . 1 '5 wavelength' 1.3847 1.3847 20.00 4.00 . 0.072 0.031 1 '5 wavelength' 1.3847 1.3784 20.00 4.00 0.040 . . 1 '5 wavelength' 1.3847 1.2862 20.00 4.00 0.059 . . 1 '5 wavelength' 1.3784 1.3784 20.00 4.00 . 0.059 0.032 1 '5 wavelength' 1.3784 1.2862 20.00 4.00 0.059 . . 1 '5 wavelength' 1.2862 1.3847 20.00 4.00 . 0.058 0.028 1 '5 wavelength' 1.3857 1.3857 4.00 3.00 . 0.078 0.075 1 '5 wavelength' 1.3857 1.3852 4.00 3.00 0.059 . . 1 '5 wavelength' 1.3857 1.3847 4.00 3.00 0.067 . . 1 '5 wavelength' 1.3857 1.3784 4.00 3.00 0.084 . . 1 '5 wavelength' 1.3857 1.2862 4.00 3.00 0.073 . . 1 '5 wavelength' 1.3852 1.3852 4.00 3.00 . 0.101 0.088 1 '5 wavelength' 1.3852 1.3847 4.00 3.00 0.066 . . 1 '5 wavelength' 1.3852 1.3784 4.00 3.00 0.082 . . 1 '5 wavelength' 1.3852 1.2862 4.00 3.00 0.085 . . 1 '5 wavelength' 1.3847 1.3847 4.00 3.00 . 0.097 0.074 1 '5 wavelength' 1.3847 1.3784 4.00 3.00 0.081 . . 1 '5 wavelength' 1.3847 1.2862 4.00 3.00 0.085 . . 1 '5 wavelength' 1.3784 1.3784 4.00 3.00 . 0.114 0.089 1 '5 wavelength' 1.3784 1.2862 4.00 3.00 0.103 . . 1 '5 wavelength' 1.2862 1.2862 4.00 3.00 . 0.062 0.060 2 '5 wavelength' 0.7263 0.7263 15.00 3.00 . 0.035 0.026 2 '5 wavelength' 0.7263 0.7251 15.00 3.00 0.028 . . 2 '5 wavelength' 0.7263 0.7284 15.00 3.00 0.023 . . 2 '5 wavelength' 0.7263 0.7246 15.00 3.00 0.025 . . 2 '5 wavelength' 0.7263 0.7217 15.00 3.00 0.026 . . 2 '5 wavelength' 0.7251 0.7251 15.00 3.00 . 0.060 0.026 2 '5 wavelength' 0.7251 0.7284 15.00 3.00 0.029 . . 2 '5 wavelength' 0.7251 0.7246 15.00 3.00 0.031 . . 2 '5 wavelength' 0.7251 0.7217 15.00 3.00 0.035 . . 2 '5 wavelength' 0.7284 0.7284 15.00 3.00 . 0.075 0.030 2 '5 wavelength' 0.7284 0.7246 15.00 3.00 0.023 . . 2 '5 wavelength' 0.7284 0.7217 15.00 3.00 0.027 . . 2 '5 wavelength' 0.7246 0.7246 15.00 3.00 . 0.069 0.026 2 '5 wavelength' 0.7246 0.7217 15.00 3.00 0.024 . . 2 '5 wavelength' 0.7217 0.7284 15.00 3.00 . 0.060 0.028 2 '5 wavelength' 0.7263 0.7263 3.00 1.90 . 0.060 0.050 2 '5 wavelength' 0.7263 0.7251 3.00 1.90 0.056 . . 2 '5 wavelength' 0.7263 0.7284 3.00 1.90 0.055 . . 2 '5 wavelength' 0.7263 0.7246 3.00 1.90 0.053 . . 2 '5 wavelength' 0.7263 0.7217 3.00 1.90 0.056 . . 2 '5 wavelength' 0.7251 0.7251 3.00 1.90 . 0.089 0.050 2 '5 wavelength' 0.7251 0.7284 3.00 1.90 0.054 . . 2 '5 wavelength' 0.7251 0.7246 3.00 1.90 0.058 . . 2 '5 wavelength' 0.7251 0.7217 3.00 1.90 0.063 . . 2 '5 wavelength' 0.7284 0.7284 3.00 1.90 . 0.104 0.057 2 '5 wavelength' 0.7284 0.7246 3.00 1.90 0.052 . . 2 '5 wavelength' 0.7284 0.7217 3.00 1.90 0.057 . . 2 '5 wavelength' 0.7246 0.7246 3.00 1.90 . 0.098 0.052 2 '5 wavelength' 0.7246 0.7217 3.00 1.90 0.054 . . 2 '5 wavelength' 0.7217 0.7284 3.00 1.90 . 0.089 0.060 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_ratio.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the highest resolution. ; _item.name '_phasing_MAD_ratio.d_res_high' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the lowest resolution. ; _item.name '_phasing_MAD_ratio.d_res_low' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.expt_id _item_description.description ; This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category. ; _item.name '_phasing_MAD_ratio.expt_id' _item.mandatory_code yes save_ save__phasing_MAD_ratio.clust_id _item_description.description ; This data item is a pointer to _phasing_MAD_clust.id in the PHASING_MAD_CLUST category. ; _item.name '_phasing_MAD_ratio.clust_id' _item.mandatory_code yes save_ save__phasing_MAD_ratio.ratio_one_wl _item_description.description ; The root-mean-square Bijvoet difference at one wavelength for all reflections. ; _item.name '_phasing_MAD_ratio.ratio_one_wl' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.ratio_one_wl_centric _item_description.description ; The root-mean-square Bijvoet difference at one wavelength for centric reflections. This would be equal to zero for perfect data and thus serves as an estimate of the noise in the anomalous signals. ; _item.name '_phasing_MAD_ratio.ratio_one_wl_centric' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.ratio_two_wl _item_description.description ; The root-mean-square dispersive Bijvoet difference between two wavelengths for all reflections. ; _item.name '_phasing_MAD_ratio.ratio_two_wl' _item.category_id phasing_MAD_ratio _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_ratio.wavelength_1 _item_description.description ; This data item is a pointer to _phasing_MAD_set.wavelength in the PHASING_MAD_SET category. ; _item.name '_phasing_MAD_ratio.wavelength_1' _item.mandatory_code yes save_ save__phasing_MAD_ratio.wavelength_2 _item_description.description ; This data item is a pointer to _phasing_MAD_set.wavelength in the PHASING_MAD_SET category. ; _item.name '_phasing_MAD_ratio.wavelength_2' _item.mandatory_code yes save_ ##################### ## PHASING_MAD_SET ## ##################### save_phasing_MAD_set _category.description ; Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment. ; _category.id phasing_MAD_set _category.mandatory_code no loop_ _category_key.name '_phasing_MAD_set.expt_id' '_phasing_MAD_set.clust_id' '_phasing_MAD_set.set_id' '_phasing_MAD_set.wavelength' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. ; ; loop_ _phasing_MAD_set.expt_id _phasing_MAD_set.clust_id _phasing_MAD_set.set_id _phasing_MAD_set.wavelength _phasing_MAD_set.wavelength_details _phasing_MAD_set.d_res_low _phasing_MAD_set.d_res_high _phasing_MAD_set.f_prime _phasing_MAD_set.f_double_prime 1 '4 wavelength' aa 1.4013 'pre-edge' 20.00 3.00 -12.48 3.80 1 '4 wavelength' bb 1.3857 'peak' 20.00 3.00 -31.22 17.20 1 '4 wavelength' cc 1.3852 'edge' 20.00 3.00 -13.97 29.17 1 '4 wavelength' dd 1.3847 'remote' 20.00 3.00 -6.67 17.34 1 '5 wavelength' ee 1.3857 'ascending edge' 20.00 3.00 -28.33 14.84 1 '5 wavelength' ff 1.3852 'peak' 20.00 3.00 -21.50 30.23 1 '5 wavelength' gg 1.3847 'descending edge' 20.00 3.00 -10.71 20.35 1 '5 wavelength' hh 1.3784 'remote 1' 20.00 3.00 -14.45 11.84 1 '5 wavelength' ii 1.2862 'remote 2' 20.00 3.00 -9.03 9.01 2 '5 wavelength' jj 0.7263 'pre-edge' 15.00 1.90 -21.10 4.08 2 '5 wavelength' kk 0.7251 'edge' 15.00 1.90 -34.72 7.92 2 '5 wavelength' ll 0.7248 'peak' 15.00 1.90 -24.87 10.30 2 '5 wavelength' mm 0.7246 'descending edge' 15.00 1.90 -17.43 9.62 2 '5 wavelength' nn 0.7217 'remote' 15.00 1.90 -13.26 8.40 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MAD_set.clust_id _item_description.description ; This data item is a pointer to _phasing_MAD_clust.id in the PHASING_MAD_CLUST category. ; _item.name '_phasing_MAD_set.clust_id' _item.mandatory_code yes save_ save__phasing_MAD_set.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data used for this set of data. This is called the highest resolution. ; _item.name '_phasing_MAD_set.d_res_high' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data used for this set of data. This is called the lowest resolution. ; _item.name '_phasing_MAD_set.d_res_low' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.expt_id _item_description.description ; This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category. ; _item.name '_phasing_MAD_set.expt_id' _item.mandatory_code yes save_ save__phasing_MAD_set.f_double_prime _item_description.description ; The f'' component of the anomalous scattering factor for this wavelength. ; _item.name '_phasing_MAD_set.f_double_prime' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.f_prime _item_description.description ; The f' component of the anomalous scattering factor for this wavelength. ; _item.name '_phasing_MAD_set.f_prime' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code float save_ save__phasing_MAD_set.set_id _item_description.description ; This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MAD_set.set_id' _item.mandatory_code yes save_ save__phasing_MAD_set.wavelength _item_description.description ; The wavelength at which this data set was measured. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MAD_set.wavelength' phasing_MAD_set yes '_phasing_MAD_ratio.wavelength_1' phasing_MAD_ratio yes '_phasing_MAD_ratio.wavelength_2' phasing_MAD_ratio yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MAD_ratio.wavelength_1' '_phasing_MAD_set.wavelength' '_phasing_MAD_ratio.wavelength_2' '_phasing_MAD_set.wavelength' _item_type.code float save_ save__phasing_MAD_set.wavelength_details _item_description.description ; A descriptor for this wavelength in this cluster of data sets. ; _item.name '_phasing_MAD_set.wavelength_details' _item.category_id phasing_MAD_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'peak' 'remote' 'ascending edge' save_ ################# ## PHASING_MIR ## ################# save_phasing_MIR _category.description ; Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS). ; _category.id phasing_MIR _category.mandatory_code no _category_key.name '_phasing_MIR.entry_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. ; ; _phasing_MIR.method ; Standard phase refinement (Blow & Crick, 1959) ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR.details _item_description.description ; A description of special aspects of the isomorphous-replacement phasing. ; _item.name '_phasing_MIR.details' _item.category_id phasing_MIR _item.mandatory_code no _item_type.code text save_ save__phasing_MIR.d_res_high _item_description.description ; The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the highest resolution. ; _item.name '_phasing_MIR.d_res_high' _item.category_id phasing_MIR _item.mandatory_code yes _item_aliases.alias_name '_phasing_MIR.ebi_d_res_high' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR.d_res_low _item_description.description ; The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the lowest resolution. ; _item.name '_phasing_MIR.d_res_low' _item.category_id phasing_MIR _item.mandatory_code yes _item_aliases.alias_name '_phasing_MIR.ebi_d_res_low' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_phasing_MIR.entry_id' _item.mandatory_code yes save_ save__phasing_MIR.FOM _item_description.description ; The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.FOM' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.FOM_acentric _item_description.description ; The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.FOM_acentric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.FOM_centric _item_description.description ; The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR.FOM_centric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_fom_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR.method _item_description.description ; A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program. ; _item.name '_phasing_MIR.method' _item.category_id phasing_MIR _item.mandatory_code no _item_type.code text save_ save__phasing_MIR.reflns _item_description.description ; The total number of reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_acentric _item_description.description ; The number of acentric reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns_acentric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_centric _item_description.description ; The number of centric reflections phased in the native data set. ; _item.name '_phasing_MIR.reflns_centric' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR.reflns_criterion _item_description.description ; Criterion used to limit the reflections used in the phasing calculations. ; _item.name '_phasing_MIR.reflns_criterion' _item.category_id phasing_MIR _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR.ebi_reflns_criteria' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code text _item_examples.case '> 4 \s(I)' save_ ##################### ## PHASING_MIR_DER ## ##################### save_phasing_MIR_der _category.description ; Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via _phasing_MIR_der.der_set_id and _phasing_MIR_der.native_set_id. ; _category.id phasing_MIR_der _category.mandatory_code no _category_key.name '_phasing_MIR_der.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. ; ; loop_ _phasing_MIR_der.id _phasing_MIR_der.number_of_sites _phasing_MIR_der.details KAu(CN)2 3 'major site interpreted in difference Patterson' K2HgI4 6 'sites found in cross-difference Fourier' K3IrCl6 2 'sites found in cross-difference Fourier' All 11 'data for all three derivatives combined' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data used for this derivative. This is called the highest resolution. ; _item.name '_phasing_MIR_der.d_res_high' _item.category_id phasing_MIR_der _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data used for this derivative. This is called the lowest resolution. ; _item.name '_phasing_MIR_der.d_res_low' _item.category_id phasing_MIR_der _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der.der_set_id _item_description.description ; The data set that was treated as the derivative in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MIR_der.der_set_id' _item.mandatory_code yes save_ save__phasing_MIR_der.details _item_description.description ; A description of special aspects of this derivative, its data, its solution or its use in phasing. ; _item.name '_phasing_MIR_der.details' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code text save_ save__phasing_MIR_der.id _item_description.description ; The value of _phasing_MIR_der.id must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_MIR_der.id' phasing_MIR_der yes '_phasing_MIR_der_refln.der_id' phasing_MIR_der_refln yes '_phasing_MIR_der_shell.der_id' phasing_MIR_der_shell yes '_phasing_MIR_der_site.der_id' phasing_MIR_der_site yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_MIR_der_refln.der_id' '_phasing_MIR_der.id' '_phasing_MIR_der_shell.der_id' '_phasing_MIR_der.id' '_phasing_MIR_der_site.der_id' '_phasing_MIR_der.id' _item_type.code line loop_ _item_examples.case 'KAu(CN)2' 'K2HgI4_anom' 'K2HgI4_iso' save_ save__phasing_MIR_der.native_set_id _item_description.description ; The data set that was treated as the native in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MIR_der.native_set_id' _item.mandatory_code yes save_ save__phasing_MIR_der.number_of_sites _item_description.description ; The number of heavy-atom sites in this derivative. ; _item.name '_phasing_MIR_der.number_of_sites' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code int save_ save__phasing_MIR_der.power_acentric _item_description.description ; The mean phasing power P for acentric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of this derivative Fph~calc~ = the calculated structure-factor amplitude of this derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der.power_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_power_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.power_centric _item_description.description ; The mean phasing power P for centric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der.power_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_power_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_acentric _item_description.description ; Residual factor R~cullis,acen~ for acentric reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis,acen~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_anomalous _item_description.description ; Residual factor R~cullis,ano~ for anomalous reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. A value less than 1.0 means there is some contribution to the phasing from the anomalous data. sum |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| R~cullis,ano~ = ------------------------------------------------ sum|Fph+~obs~ - Fph-~obs~| Fph+~obs~ = the observed positive Friedel structure-factor amplitude for the derivative Fph-~obs~ = the observed negative Friedel structure-factor amplitude for the derivative Fh+~calc~ = the calculated positive Friedel structure-factor amplitude from the heavy-atom model Fh-~calc~ = the calculated negative Friedel structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_anomalous' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_anomalous' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.R_cullis_centric _item_description.description ; Residual factor R~cullis~ for centric reflections for this derivative. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der.R_cullis_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der.reflns_acentric _item_description.description ; The number of acentric reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_acentric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_anomalous _item_description.description ; The number of anomalous reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_anomalous' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_anomalous' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_centric _item_description.description ; The number of centric reflections used in phasing for this derivative. ; _item.name '_phasing_MIR_der.reflns_centric' _item.category_id phasing_MIR_der _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_der.reflns_criteria _item_description.description ; Criteria used to limit the reflections used in the phasing calculations. ; _item.name '_phasing_MIR_der.reflns_criteria' _item.category_id phasing_MIR_der _item.mandatory_code no _item_type.code text _item_examples.case '> 4 \s(I)' save_ ########################### ## PHASING_MIR_DER_REFLN ## ########################### save_phasing_MIR_der_refln _category.description ; Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_refln.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness. ; _category.id phasing_MIR_der_refln _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_refln.index_h' '_phasing_MIR_der_refln.index_k' '_phasing_MIR_der_refln.index_l' '_phasing_MIR_der_refln.der_id' '_phasing_MIR_der_refln.set_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the 6,1,25 reflection of an Hg/Pt derivative of protein NS1. ; ; _phasing_MIR_der_refln.index_h 6 _phasing_MIR_der_refln.index_k 1 _phasing_MIR_der_refln.index_l 25 _phasing_MIR_der_refln.der_id HGPT1 _phasing_MIR_der_refln.set_id 'NS1-96' _phasing_MIR_der_refln.F_calc_au 106.66 _phasing_MIR_der_refln.F_meas_au 204.67 _phasing_MIR_der_refln.F_meas_sigma 6.21 _phasing_MIR_der_refln.HL_A_iso -3.15 _phasing_MIR_der_refln.HL_B_iso -0.76 _phasing_MIR_der_refln.HL_C_iso 0.65 _phasing_MIR_der_refln.HL_D_iso 0.23 _phasing_MIR_der_refln.phase_calc 194.48 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der_refln.der_id _item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _item.name '_phasing_MIR_der_refln.der_id' _item.mandatory_code yes save_ save__phasing_MIR_der_refln.F_calc _item_description.description ; The calculated value of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_der_refln.F_calc' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_related.related_name '_phasing_MIR_der_refln.F_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__phasing_MIR_der_refln.F_calc_au _item_description.description ; The calculated value of the structure factor for this derivative, in arbitrary units. ; _item.name '_phasing_MIR_der_refln.F_calc_au' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_related.related_name '_phasing_MIR_der_refln.F_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__phasing_MIR_der_refln.F_meas _item_description.description ; The measured value of the structure factor for this derivative, in electrons. ; _item.name '_phasing_MIR_der_refln.F_meas' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas_sigma' associated_esd '_phasing_MIR_der_refln.F_meas_au' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code electrons save_ save__phasing_MIR_der_refln.F_meas_au _item_description.description ; The measured value of the structure factor for this derivative, in arbitrary units. ; _item.name '_phasing_MIR_der_refln.F_meas_au' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas_sigma_au' associated_esd '_phasing_MIR_der_refln.F_meas' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__phasing_MIR_der_refln.F_meas_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas, in electrons. ; _item.name '_phasing_MIR_der_refln.F_meas_sigma' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas' associated_value '_phasing_MIR_der_refln.F_meas_sigma_au' conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__phasing_MIR_der_refln.F_meas_sigma_au _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas_au, in arbitrary units. ; _item.name '_phasing_MIR_der_refln.F_meas_sigma_au' _item.category_id phasing_MIR_der_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_MIR_der_refln.F_meas_au' associated_value '_phasing_MIR_der_refln.F_meas_sigma' conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__phasing_MIR_der_refln.HL_A_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the calculated phase from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_A_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.HL_B_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_B_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.HL_C_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)^2^ - cos(alphah~calc~)^2^] C~iso~ = ------------------------------------ E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_C_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.HL_D_iso _item_description.description ; The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^ * cos(alphah~calc~)^2^ D~iso~ = ---------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. ; _item.name '_phasing_MIR_der_refln.HL_D_iso' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_refln.index_h _item_description.description ; Miller index h for this reflection for this derivative. ; _item.name '_phasing_MIR_der_refln.index_h' _item.category_id phasing_MIR_der_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_MIR_der_refln.index_k' '_phasing_MIR_der_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_MIR_der_refln.index_k _item_description.description ; Miller index k for this reflection for this derivative. ; _item.name '_phasing_MIR_der_refln.index_k' _item.category_id phasing_MIR_der_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_MIR_der_refln.index_h' '_phasing_MIR_der_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_MIR_der_refln.index_l _item_description.description ; Miller index l for this reflection for this derivative. ; _item.name '_phasing_MIR_der_refln.index_l' _item.category_id phasing_MIR_der_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_MIR_der_refln.index_h' '_phasing_MIR_der_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_MIR_der_refln.phase_calc _item_description.description ; The calculated value of the structure-factor phase based on the heavy-atom model for this derivative in degrees. ; _item.name '_phasing_MIR_der_refln.phase_calc' _item.category_id phasing_MIR_der_refln _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__phasing_MIR_der_refln.set_id _item_description.description ; This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_MIR_der_refln.set_id' _item.mandatory_code yes save_ ########################### ## PHASING_MIR_DER_SHELL ## ########################### save_phasing_MIR_der_shell _category.description ; Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_shell.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) ; _category.id phasing_MIR_der_shell _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_shell.der_id' '_phasing_MIR_der_shell.d_res_low' '_phasing_MIR_der_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. ; ; loop_ _phasing_MIR_der_shell.der_id _phasing_MIR_der_shell.d_res_low _phasing_MIR_der_shell.d_res_high _phasing_MIR_der_shell.ha_ampl _phasing_MIR_der_shell.loc KAu(CN)2 15.0 8.3 54 26 KAu(CN)2 8.3 6.4 54 20 KAu(CN)2 6.4 5.2 50 20 KAu(CN)2 5.2 4.4 44 23 KAu(CN)2 4.4 3.8 39 23 KAu(CN)2 3.8 3.4 33 21 KAu(CN)2 3.4 3.0 28 17 KAu(CN)2 15.0 3.0 38 21 K2HgI4 15.0 8.3 149 87 K2HgI4 8.3 6.4 121 73 K2HgI4 6.4 5.2 95 61 K2HgI4 5.2 4.4 80 60 K2HgI4 4.4 3.8 73 63 K2HgI4 3.8 3.4 68 57 K2HgI4 3.4 3.0 63 46 K2HgI4 15.0 3.0 79 58 K3IrCl6 15.0 8.3 33 27 K3IrCl6 8.3 6.4 40 23 K3IrCl6 6.4 5.2 31 22 K3IrCl6 5.2 4.4 27 23 K3IrCl6 4.4 3.8 22 23 K3IrCl6 3.8 3.4 19 20 K3IrCl6 3.4 3.0 16 20 K3IrCl6 15.0 3.0 23 21 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der_shell.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the highest resolution. ; _item.name '_phasing_MIR_der_shell.d_res_high' _item.category_id phasing_MIR_der_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_shell.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the lowest resolution. ; _item.name '_phasing_MIR_der_shell.d_res_low' _item.category_id phasing_MIR_der_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_shell.der_id _item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _item.name '_phasing_MIR_der_shell.der_id' _item.mandatory_code yes save_ save__phasing_MIR_der_shell.fom _item_description.description ; The mean value of the figure of merit m for reflections for this derivative in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_der_shell.fom' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.ha_ampl _item_description.description ; The mean heavy-atom amplitude for reflections for this derivative in this shell. ; _item.name '_phasing_MIR_der_shell.ha_ampl' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.loc _item_description.description ; The mean lack-of-closure error loc for reflections for this derivative in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections ; _item.name '_phasing_MIR_der_shell.loc' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.phase _item_description.description ; The mean of the phase values for reflections for this derivative in this shell. ; _item.name '_phasing_MIR_der_shell.phase' _item.category_id phasing_MIR_der_shell _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_der_shell.power _item_description.description ; The mean phasing power P for reflections for this derivative in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_der_shell.power' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.R_cullis _item_description.description ; Residual factor R~cullis~ for centric reflections for this derivative in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_der_shell.R_cullis' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.R_kraut _item_description.description ; Residual factor R~kraut~ for general reflections for this derivative in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. ; _item.name '_phasing_MIR_der_shell.R_kraut' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_shell.reflns _item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_der_shell.reflns' _item.category_id phasing_MIR_der_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ########################## ## PHASING_MIR_DER_SITE ## ########################## save_phasing_MIR_der_site _category.description ; Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_site.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) ; _category.id phasing_MIR_der_site _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_der_site.der_id' '_phasing_MIR_der_site.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with occupancies converted from electrons to fractional. ; ; loop_ _phasing_MIR_der_site.der_id _phasing_MIR_der_site.id _phasing_MIR_der_site.atom_type_symbol _phasing_MIR_der_site.occupancy _phasing_MIR_der_site.fract_x _phasing_MIR_der_site.fract_y _phasing_MIR_der_site.fract_z _phasing_MIR_der_site.B_iso KAu(CN)2 1 Au 0.40 0.082 0.266 0.615 33.0 KAu(CN)2 2 Au 0.03 0.607 0.217 0.816 25.9 KAu(CN)2 3 Au 0.02 0.263 0.782 0.906 15.7 K2HgI4 1 Hg 0.63 0.048 0.286 0.636 33.7 K2HgI4 2 Hg 0.34 0.913 0.768 0.889 36.7 K2HgI4 3 Hg 0.23 0.974 0.455 0.974 24.2 K2HgI4 4 Hg 0.28 0.903 0.836 0.859 14.7 K2HgI4 5 Hg 0.07 0.489 0.200 0.885 6.4 K2HgI4 6 Hg 0.07 0.162 0.799 0.889 32.9 K3IrCl6 1 Ir 0.26 0.209 0.739 0.758 40.8 K3IrCl6 2 Ir 0.05 0.279 0.613 0.752 24.9 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_der_site.atom_type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy-atom data; in some cases this is the scattering factor for the single heavy atom, in other cases these are the scattering factors for an atomic cluster. ; _item.name '_phasing_MIR_der_site.atom_type_symbol' _item.mandatory_code yes save_ save__phasing_MIR_der_site.B_iso _item_description.description ; Isotropic displacement parameter for this heavy-atom site in this derivative. ; _item.name '_phasing_MIR_der_site.B_iso' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_related.related_name '_phasing_MIR_der_site.B_iso_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.B_iso_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.B_iso. ; _item.name '_phasing_MIR_der_site.B_iso_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.B_iso' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_x _item_description.description ; The x coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_phasing_MIR_der_site.Cartn_x' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_y' '_phasing_MIR_der_site.Cartn_z' _item_related.related_name '_phasing_MIR_der_site.Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_x. ; _item.name '_phasing_MIR_der_site.Cartn_x_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_y_esd' '_phasing_MIR_der_site.Cartn_z_esd' _item_related.related_name '_phasing_MIR_der_site.Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_y _item_description.description ; The y coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_phasing_MIR_der_site.Cartn_y' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x' '_phasing_MIR_der_site.Cartn_z' _item_related.related_name '_phasing_MIR_der_site.Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_y. ; _item.name '_phasing_MIR_der_site.Cartn_y_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x_esd' '_phasing_MIR_der_site.Cartn_z_esd' _item_related.related_name '_phasing_MIR_der_site.Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_z _item_description.description ; The z coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_phasing_MIR_der_site.Cartn_z' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x' '_phasing_MIR_der_site.Cartn_y' _item_related.related_name '_phasing_MIR_der_site.Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__phasing_MIR_der_site.Cartn_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_z. ; _item.name '_phasing_MIR_der_site.Cartn_z_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.Cartn_x_esd' '_phasing_MIR_der_site.Cartn_y_esd' _item_related.related_name '_phasing_MIR_der_site.Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_der_site.der_id _item_description.description ; This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category. ; _item.name '_phasing_MIR_der_site.der_id' _item.mandatory_code yes save_ save__phasing_MIR_der_site.details _item_description.description ; A description of special aspects of the derivative site. ; _item.name '_phasing_MIR_der_site.details' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'binds to His 117' 'minor site obtained from difference Fourier' 'same as site 2 in the K2HgI4 derivative' save_ save__phasing_MIR_der_site.fract_x _item_description.description ; The x coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_a. ; _item.name '_phasing_MIR_der_site.fract_x' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_y' '_phasing_MIR_der_site.fract_z' _item_related.related_name '_phasing_MIR_der_site.fract_x_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.fract_x_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_x. ; _item.name '_phasing_MIR_der_site.fract_x_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_y_esd' '_phasing_MIR_der_site.fract_z_esd' _item_related.related_name '_phasing_MIR_der_site.fract_x' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__phasing_MIR_der_site.fract_y _item_description.description ; The y coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_b. ; _item.name '_phasing_MIR_der_site.fract_y' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x' '_phasing_MIR_der_site.fract_z' _item_related.related_name '_phasing_MIR_der_site.fract_y_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.fract_y_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_y. ; _item.name '_phasing_MIR_der_site.fract_y_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x_esd' '_phasing_MIR_der_site.fract_z_esd' _item_related.related_name '_phasing_MIR_der_site.fract_y' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__phasing_MIR_der_site.fract_z _item_description.description ; The z coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_c. ; _item.name '_phasing_MIR_der_site.fract_z' _item.category_id phasing_MIR_der_site _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x' '_phasing_MIR_der_site.fract_y' _item_related.related_name '_phasing_MIR_der_site.fract_z_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.fract_z_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_z. ; _item.name '_phasing_MIR_der_site.fract_z_esd' _item.category_id phasing_MIR_der_site _item.mandatory_code no # _item_default.value 0.0 loop_ _item_dependent.dependent_name '_phasing_MIR_der_site.fract_x_esd' '_phasing_MIR_der_site.fract_y_esd' _item_related.related_name '_phasing_MIR_der_site.fract_z' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__phasing_MIR_der_site.id _item_description.description ; The value of _phasing_MIR_der_site.id must uniquely identify each site in each derivative in the PHASING_MIR_DER_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_phasing_MIR_der_site.id' _item.category_id phasing_MIR_der_site _item.mandatory_code yes _item_type.code code save_ save__phasing_MIR_der_site.occupancy _item_description.description ; The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_phasing_MIR_der_site.occupancy' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_der_site.occupancy_anom _item_description.description ; The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. ; _item.name '_phasing_MIR_der_site.occupancy_anom' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_anom_su' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.occupancy_anom_su _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.occupancy_anom. ; _item.name '_phasing_MIR_der_site.occupancy_anom_su' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom_esd' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 # _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_anom' _item_related.function_code associated_value _item_type.code float save_ save__phasing_MIR_der_site.occupancy_iso _item_description.description ; The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. ; _item.name '_phasing_MIR_der_site.occupancy_iso' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_iso_su' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__phasing_MIR_der_site.occupancy_iso_su _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.occupancy_iso. ; _item.name '_phasing_MIR_der_site.occupancy_iso_su' _item.category_id phasing_MIR_der_site _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso_esd' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 # _item_default.value 0.0 _item_related.related_name '_phasing_MIR_der_site.occupancy_iso' _item_related.function_code associated_value _item_type.code float save_ ####################### ## PHASING_MIR_SHELL ## ####################### save_phasing_MIR_shell _category.description ; Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution. ; _category.id phasing_MIR_shell _category.mandatory_code no loop_ _category_key.name '_phasing_MIR_shell.d_res_low' '_phasing_MIR_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. ; ; loop_ _phasing_MIR_shell.d_res_low _phasing_MIR_shell.d_res_high _phasing_MIR_shell.reflns _phasing_MIR_shell.FOM 15.0 8.3 80 0.69 8.3 6.4 184 0.73 6.4 5.2 288 0.72 5.2 4.4 406 0.65 4.4 3.8 554 0.54 3.8 3.4 730 0.53 3.4 3.0 939 0.50 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_MIR_shell.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. ; _item.name '_phasing_MIR_shell.d_res_high' _item.category_id phasing_MIR_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_shell.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low. ; _item.name '_phasing_MIR_shell.d_res_low' _item.category_id phasing_MIR_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_MIR_shell.FOM _item_description.description ; The mean value of the figure of merit m for reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.FOM' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.FOM_acentric _item_description.description ; The mean value of the figure of merit m for acentric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.FOM_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.FOM_centric _item_description.description ; The mean value of the figure of merit m for centric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. ; _item.name '_phasing_MIR_shell.FOM_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.loc _item_description.description ; The mean lack-of-closure error loc for reflections in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections ; _item.name '_phasing_MIR_shell.loc' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.mean_phase _item_description.description ; The mean of the phase values for all reflections in this shell. ; _item.name '_phasing_MIR_shell.mean_phase' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_type.code float save_ save__phasing_MIR_shell.power _item_description.description ; The mean phasing power P for reflections in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections ; _item.name '_phasing_MIR_shell.power' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.R_cullis _item_description.description ; Residual factor R~cullis~ for centric reflections in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. ; _item.name '_phasing_MIR_shell.R_cullis' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.R_kraut _item_description.description ; Residual factor R~kraut~ for general reflections in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. ; _item.name '_phasing_MIR_shell.R_kraut' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__phasing_MIR_shell.reflns _item_description.description ; The number of reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns' _item.category_id phasing_MIR_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_acentric _item_description.description ; The number of acentric reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_acentric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_acentric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_anomalous _item_description.description ; The number of anomalous reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_anomalous' _item.category_id phasing_MIR_shell _item.mandatory_code no # _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_anomalous' # _item_aliases.dictionary ebi_extensions # _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__phasing_MIR_shell.reflns_centric _item_description.description ; The number of centric reflections in this shell. ; _item.name '_phasing_MIR_shell.reflns_centric' _item.category_id phasing_MIR_shell _item.mandatory_code no _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_centric' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ ################# ## PHASING_SET ## ################# save_phasing_set _category.description ; Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block. ; _category.id phasing_set _category.mandatory_code no _category_key.name '_phasing_set.id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for an Hg/Pt derivative of protein NS1. ; ; _phasing_set.id 'NS1-96' _phasing_set.cell_angle_alpha 90.0 _phasing_set.cell_angle_beta 90.0 _phasing_set.cell_angle_gamma 90.0 _phasing_set.cell_length_a 38.63 _phasing_set.cell_length_b 38.63 _phasing_set.cell_length_c 82.88 _phasing_set.radiation_wavelength 1.5145 _phasing_set.detector_type 'image plate' _phasing_set.detector_specific 'RXII' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_set.cell_angle_alpha _item_description.description ; Unit-cell angle alpha for this data set in degrees. ; _item.name '_phasing_set.cell_angle_alpha' _item.category_id phasing_set _item.mandatory_code no _item_default.value 90.0 loop_ _item_dependent.dependent_name '_phasing_set.cell_angle_beta' '_phasing_set.cell_angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_sub_category.id cell_angle _item_type.code float _item_units.code degrees save_ save__phasing_set.cell_angle_beta _item_description.description ; Unit-cell angle beta for this data set in degrees. ; _item.name '_phasing_set.cell_angle_beta' _item.category_id phasing_set _item.mandatory_code no _item_default.value 90.0 loop_ _item_dependent.dependent_name '_phasing_set.cell_angle_alpha' '_phasing_set.cell_angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_sub_category.id cell_angle _item_type.code float _item_units.code degrees save_ save__phasing_set.cell_angle_gamma _item_description.description ; Unit-cell angle gamma for this data set in degrees. ; _item.name '_phasing_set.cell_angle_gamma' _item.category_id phasing_set _item.mandatory_code no _item_default.value 90.0 loop_ _item_dependent.dependent_name '_phasing_set.cell_angle_alpha' '_phasing_set.cell_angle_beta' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_sub_category.id cell_angle _item_type.code float _item_units.code degrees save_ save__phasing_set.cell_length_a _item_description.description ; Unit-cell length a for this data set in angstroms. ; _item.name '_phasing_set.cell_length_a' _item.category_id phasing_set _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_set.cell_length_b' '_phasing_set.cell_length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_sub_category.id cell_length _item_type.code float _item_units.code angstroms save_ save__phasing_set.cell_length_b _item_description.description ; Unit-cell length b for this data set in angstroms. ; _item.name '_phasing_set.cell_length_b' _item.category_id phasing_set _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_set.cell_length_a' '_phasing_set.cell_length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_sub_category.id cell_length _item_type.code float _item_units.code angstroms save_ save__phasing_set.cell_length_c _item_description.description ; Unit-cell length c for this data set in angstroms. ; _item.name '_phasing_set.cell_length_c' _item.category_id phasing_set _item.mandatory_code no loop_ _item_dependent.dependent_name '_phasing_set.cell_length_a' '_phasing_set.cell_length_b' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_sub_category.id cell_length _item_type.code float _item_units.code angstroms save_ save__phasing_set.detector_specific _item_description.description ; The particular radiation detector. In general, this will be a manufacturer, description, model number or some combination of these. ; _item.name '_phasing_set.detector_specific' _item.category_id phasing_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Siemens model x' 'Kodak XG' 'MAR Research model y' save_ save__phasing_set.detector_type _item_description.description ; The general class of the radiation detector. ; _item.name '_phasing_set.detector_type' _item.category_id phasing_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'multiwire' 'imaging plate' 'CCD' 'film' save_ save__phasing_set.id _item_description.description ; The value of _phasing_set.id must uniquely identify a record in the PHASING_SET list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_phasing_set.id' phasing_set yes '_phasing_set_refln.set_id' phasing_set_refln yes '_phasing_MAD_set.set_id' phasing_MAD_set yes '_phasing_MIR_der.der_set_id' phasing_MIR_der yes '_phasing_MIR_der.native_set_id' phasing_MIR_der yes '_phasing_MIR_der_refln.set_id' phasing_MIR_der_refln yes loop_ _item_linked.child_name _item_linked.parent_name '_phasing_set_refln.set_id' '_phasing_set.id' '_phasing_MAD_set.set_id' '_phasing_set.id' '_phasing_MIR_der.der_set_id' '_phasing_set.id' '_phasing_MIR_der.native_set_id' '_phasing_set.id' '_phasing_MIR_der_refln.set_id' '_phasing_set.id' _item_type.code line loop_ _item_examples.case 'KAu(CN)2' 'K2HgI4' save_ save__phasing_set.radiation_source_specific _item_description.description ; The particular source of radiation. In general, this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources. ; _item.name '_phasing_set.radiation_source_specific' _item.category_id phasing_set _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Rigaku RU200' 'Philips fine focus Mo' 'NSLS beamline X8C' save_ save__phasing_set.radiation_wavelength _item_description.description ; The mean wavelength of the radiation used to measure this data set. ; _item.name '_phasing_set.radiation_wavelength' _item.category_id phasing_set _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__phasing_set.temp _item_description.description ; The temperature in kelvins at which the data set was measured. ; _item.name '_phasing_set.temp' _item.category_id phasing_set _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code kelvins save_ ####################### ## PHASING_SET_REFLN ## ####################### save_phasing_set_refln _category.description ; Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; _phasing_set_refln.set_id indicates the data set to which a given record corresponds. ; _category.id phasing_set_refln _category.mandatory_code no loop_ _category_key.name '_phasing_set_refln.index_h' '_phasing_set_refln.index_k' '_phasing_set_refln.index_l' '_phasing_set_refln.set_id' loop_ _category_group.id 'inclusive_group' 'phasing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the 15,15,32 reflection of an Hg/Pt derivative of protein NS1. ; ; _phasing_set_refln.set_id 'NS1-96' _phasing_set_refln.index_h 15 _phasing_set_refln.index_k 15 _phasing_set_refln.index_l 32 _phasing_set_refln.F_meas_au 181.79 _phasing_set_refln.F_meas_sigma_au 3.72 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__phasing_set_refln.set_id _item_description.description ; This data item is a pointer to _phasing_set.id in the PHASING_SET category. ; _item.name '_phasing_set_refln.set_id' _item.mandatory_code yes save_ save__phasing_set_refln.F_meas _item_description.description ; The measured value of the structure factor for this reflection in this data set in electrons. ; _item.name '_phasing_set_refln.F_meas' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas_sigma' associated_esd '_phasing_set_refln.F_meas_au' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code electrons save_ save__phasing_set_refln.F_meas_au _item_description.description ; The measured value of the structure factor for this reflection in this data set in arbitrary units. ; _item.name '_phasing_set_refln.F_meas_au' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas_sigma_au' associated_esd '_phasing_set_refln.F_meas' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__phasing_set_refln.F_meas_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_set_refln.F_meas in electrons. ; _item.name '_phasing_set_refln.F_meas_sigma' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas' associated_value '_phasing_set_refln.F_meas_sigma_au' conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__phasing_set_refln.F_meas_sigma_au _item_description.description ; The standard uncertainty (estimated standard deviation) of _phasing_set_refln.F_meas_au in arbitrary units. ; _item.name '_phasing_set_refln.F_meas_sigma_au' _item.category_id phasing_set_refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_phasing_set_refln.F_meas_au' associated_value '_phasing_set_refln.F_meas_sigma' conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__phasing_set_refln.index_h _item_description.description ; Miller index h of this reflection in this data set. ; _item.name '_phasing_set_refln.index_h' _item.category_id phasing_set_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_set_refln.index_k' '_phasing_set_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_set_refln.index_k _item_description.description ; Miller index k of this reflection in this data set. ; _item.name '_phasing_set_refln.index_k' _item.category_id phasing_set_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_set_refln.index_h' '_phasing_set_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__phasing_set_refln.index_l _item_description.description ; Miller index l of this reflection in this data set. ; _item.name '_phasing_set_refln.index_l' _item.category_id phasing_set_refln _item.mandatory_code yes loop_ _item_dependent.dependent_name '_phasing_set_refln.index_h' '_phasing_set_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ ########## ## PUBL ## ########## save_publ _category.description ; Data items in the PUBL category are used when submitting a manuscript for publication. ; _category.id publ _category.mandatory_code no _category_key.name '_publ.entry_id' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _publ.section_title ; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)- 1,3-oxazolidin-5-one ; _publ.section_abstract ; The oxazolidinone ring is a shallow envelope conformation with the tert-butyl and iso-butyl groups occupying trans-positions with respect to the ring. The angles at the N atom sum to 356.2\%, indicating a very small degree of pyramidalization at this atom. This is consistent with electron delocalization between the N atom and the carbonyl centre [N-C=O = 1.374(3)\%A]. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick, Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527]. ; ; _publ.section_title ; Hemiasterlin methyl ester ; _publ.section_title_footnote ; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl- 2-methylamino-3-(N-methylbenzo[b]pyrrol- 3-yl)butanamido]-3,3-dimethyl-N-methyl- butanamido}-2-hexenoate. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_publ.entry_id' _item.mandatory_code yes save_ save__publ.contact_author _item_description.description ; The name and address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. It is preferable to use the separate data items _publ.contact_author_name and _publ.contact_author_address. ; _item.name '_publ.contact_author' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Professor George Ferguson Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 ; save_ save__publ.contact_author_address _item_description.description ; The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. ; _item.name '_publ.contact_author_address' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 ; save_ save__publ.contact_author_email _item_description.description ; E-mail address in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; _item.name '_publ.contact_author_email' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'name@host.domain.country' 'uur5@banjo.bitnet' save_ save__publ.contact_author_fax _item_description.description ; Facsimile telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. ; _item.name '_publ.contact_author_fax' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_fax' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' save_ save__publ.contact_author_name _item_description.description ; The name of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. ; _item.name '_publ.contact_author_name' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Professor George Ferguson ; save_ save__publ.contact_author_phone _item_description.description ; Telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. ; _item.name '_publ.contact_author_phone' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_author_phone' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' '12(34)9477330x5543' save_ save__publ.contact_letter _item_description.description ; A letter submitted to the journal editor by the contact author. ; _item.name '_publ.contact_letter' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_contact_letter' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.manuscript_creation _item_description.description ; A description of the word-processor package and computer used to create the word-processed manuscript stored as _publ.manuscript_processed. ; _item.name '_publ.manuscript_creation' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_creation' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Tex file created by FrameMaker on a Sun 3/280' save_ save__publ.manuscript_processed _item_description.description ; The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item _publ.manuscript_creation. ; _item.name '_publ.manuscript_processed' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_processed' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.manuscript_text _item_description.description ; The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text. ; _item.name '_publ.manuscript_text' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_text' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.requested_category _item_description.description ; The category of paper submitted. For submission to Acta Crystallographica Section C or Acta Crystallographica Section E, ONLY the codes indicated for use with these journals should be used. ; _item.name '_publ.requested_category' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_requested_category' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value FA _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail FA 'Full article' FI 'Full submission - inorganic (Acta C)' FO 'Full submission - organic (Acta C)' FM 'Full submission - metal-organic (Acta C)' CI 'CIF-access paper - inorganic (Acta C) (no longer in use)' CO 'CIF-access paper - organic (Acta C) (no longer in use)' CM 'CIF-access paper - metal-organic (Acta C) (no longer in use)' EI 'Electronic submission - inorganic (Acta E)' EO 'Electronic submission - organic (Acta E)' EM 'Electronic submission - metal-organic (Acta E)' AD 'Addenda and Errata (Acta C, Acta E)' SC 'Short communication' save_ save__publ.requested_coeditor_name _item_description.description ; The name of the co-editor whom the authors would like to handle the submitted manuscript. ; _item.name '_publ.requested_coeditor_name' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_requested_coeditor_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__publ.requested_journal _item_description.description ; The name of the journal to which the manuscript is being submitted. ; _item.name '_publ.requested_journal' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_requested_journal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__publ.section_abstract _item_description.description ; The abstract section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_abstract' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_abstract' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_acknowledgements _item_description.description ; The acknowledgements section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_acknowledgements' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_acknowledgements' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_comment _item_description.description ; The comment section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_comment' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_comment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_discussion _item_description.description ; The discussion section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_discussion' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_discussion' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_experimental _item_description.description ; The experimental section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The _publ.section_exptl_prep, _publ.section_exptl_solution and _publ.section_exptl_refinement items are preferred for separating the chemical preparation, structure solution and refinement aspects of the description of the experiment. ; _item.name '_publ.section_experimental' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_experimental' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_exptl_prep _item_description.description ; The experimental preparation section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_exptl_prep' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_prep' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_exptl_refinement _item_description.description ; The experimental refinement section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_exptl_refinement' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_refinement' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_exptl_solution _item_description.description ; The experimental solution section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_exptl_solution' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_exptl_solution' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_figure_captions _item_description.description ; The figure captions section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_figure_captions' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_figure_captions' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_introduction _item_description.description ; The introduction section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_introduction' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_introduction' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_references _item_description.description ; The references section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_references' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_references' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_synopsis _item_description.description ; The synopsis section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_synopsis' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_synopsis' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_table_legends _item_description.description ; The table legends section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_table_legends' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_table_legends' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_title _item_description.description ; The title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_title' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ.section_title_footnote _item_description.description ; The footnote to the title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. ; _item.name '_publ.section_title_footnote' _item.category_id publ _item.mandatory_code no _item_aliases.alias_name '_publ_section_title_footnote' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ################# ## PUBL_AUTHOR ## ################# save_publ_author _category.description ; Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication. ; _category.id publ_author _category.mandatory_code no _category_key.name '_publ_author.name' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; loop_ _publ_author.name _publ_author.address 'Willis, Anthony C.' ; Research School of Chemistry Australian National University GPO Box 4 Canberra, A.C.T. Australia 2601 ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ_author.address _item_description.description ; The address of a publication author. If there is more than one author this is looped with _publ_author.name. ; _item.name '_publ_author.address' _item.category_id publ_author _item.mandatory_code no _item_aliases.alias_name '_publ_author_address' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__publ_author.email _item_description.description ; The e-mail address of a publication author. If there is more than one author, this will be looped with _publ_author.name. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. ; _item.name '_publ_author.email' _item.category_id publ_author _item.mandatory_code no _item_aliases.alias_name '_publ_author_email' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.3.1 _item_type.code text loop_ _item_examples.case name@host.domain.country bm@iucr.org save_ save__publ_author.footnote _item_description.description ; A footnote accompanying an author's name in the list of authors of a paper. Typically indicates sabbatical address, additional affiliations or date of decease. ; _item.name '_publ_author.footnote' _item.category_id publ_author _item.mandatory_code no _item_aliases.alias_name '_publ_author_footnote' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'On leave from U. Western Australia' 'Also at Department of Biophysics' save_ save__publ_author.name _item_description.description ; The name of a publication author. If there are multiple authors this will be looped with _publ_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first names or initials. ; _item.name '_publ_author.name' _item.category_id publ_author _item.mandatory_code yes _item_aliases.alias_name '_publ_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' 'O'Neil, F.K.' 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A.' save_ ############### ## PUBL_BODY ## ############### save_publ_body _category.description ; Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors. ; _category.id publ_body _category.mandatory_code no loop_ _category_key.name '_publ_body.element' '_publ_body.label' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on a paper by R. Restori & D. Schwarzenbach [Acta Cryst. (1996), A52, 369-378]. ; ; loop_ _publ_body.element _publ_body.label _publ_body.title _publ_body.format _publ_body.contents section 1 Introduction cif ; X-ray diffraction from a crystalline material provides information on the thermally and spatially averaged electron density in the crystal... ; section 2 Theory tex ; In the rigid-atom approximation, the dynamic electron density of an atom is described by the convolution product of the static atomic density and a probability density function, $\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$ ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens [Acta Cryst. (1996), A52, 397-407]. ; ; loop_ _publ_body.element _publ_body.label _publ_body.title _publ_body.contents section 3 ; The two-channel method for retrieval of the deformation electron density ; . subsection 3.1 'The two-channel entropy S[\D\r(r)]' ; As the wide dynamic range involved in the total electron density... ; subsection 3.2 'Uniform vs informative prior model densities' . subsubsection 3.2.1 'Use of uniform models' ; Straightforward algebra leads to expressions analogous to... ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ_body.contents _item_description.description ; A text section of a paper. ; _item.name '_publ_body.contents' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_contents' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__publ_body.element _item_description.description ; The functional role of the associated text section. ; _item.name '_publ_body.element' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_element' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_enumeration.value 'section' 'subsection' 'subsubsection' 'appendix' 'footnote' save_ save__publ_body.format _item_description.description ; Code indicating the appropriate typesetting conventions for accented characters and special symbols in the text section. ; _item.name '_publ_body.format' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_format' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail ascii 'no coding for special symbols' cif 'CIF convention' latex 'LaTeX' sgml 'SGML (ISO 8879)' tex 'TeX' troff 'troff or nroff' save_ save__publ_body.label _item_description.description ; Code identifying the section of text. ; _item.name '_publ_body.label' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_examples.case '1' '1.1' '2.1.3' save_ save__publ_body.title _item_description.description ; Title of the associated section of text. ; _item.name '_publ_body.title' _item.category_id publ_body _item.mandatory_code no _item_aliases.alias_name '_publ_body_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ########################## ## PUBL_MANUSCRIPT_INCL ## ########################## save_publ_manuscript_incl _category.description ; Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software. ; _category.id publ_manuscript_incl _category.mandatory_code no _category_key.name '_publ_manuscript_incl.entry_id' loop_ _category_group.id 'inclusive_group' 'iucr_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; _publ_manuscript_incl.entry_id 'EXAMHYPO' loop_ _publ_manuscript_incl.extra_item _publ_manuscript_incl.extra_info _publ_manuscript_incl.extra_defn '_atom_site.symmetry_multiplicity' 'to emphasise special sites' yes '_chemical.compound_source' 'rare material, unusual source' yes '_reflns.d_resolution_high' 'limited data is a problem here' yes '_crystal.magnetic_permeability' 'unusual value for this material' no ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__publ_manuscript_incl.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_publ_manuscript_incl.entry_id' _item.mandatory_code yes save_ save__publ_manuscript_incl.extra_defn _item_description.description ; Flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not. ; _item.name '_publ_manuscript_incl.extra_defn' _item.category_id publ_manuscript_incl _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_defn' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail no 'not a standard CIF data name' n 'abbreviation for "no"' yes 'a standard CIF data name' y 'abbreviation for "yes"' save_ save__publ_manuscript_incl.extra_info _item_description.description ; A short note indicating the reason why the author wishes the corresponding data item marked for inclusion in the journal request list to be published. ; _item.name '_publ_manuscript_incl.extra_info' _item.category_id publ_manuscript_incl _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_info' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text loop_ _item_examples.case 'to emphasise very special sites' 'rare material from unusual source' 'the limited data is a problem here' 'a new data quantity needed here' save_ save__publ_manuscript_incl.extra_item _item_description.description ; Specifies the inclusion of specific data into a manuscript which are not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list. ; _item.name '_publ_manuscript_incl.extra_item' _item.category_id publ_manuscript_incl _item.mandatory_code no _item_aliases.alias_name '_publ_manuscript_incl_extra_item' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '_atom_site.symmetry_multiplicity' '_chemical.compound_source' '_reflns.d_resolution_high' '_crystal.magnetic_permeability' save_ ############ ## REFINE ## ############ save_refine _category.description ; Data items in the REFINE category record details about the structure-refinement parameters. ; _category.id refine _category.mandatory_code no _category_key.name '_refine.entry_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _refine.entry_id '5HVP' _refine.ls_number_reflns_obs 12901 _refine.ls_number_restraints 6609 _refine.ls_number_parameters 7032 _refine.ls_R_Factor_obs 0.176 _refine.ls_weighting_scheme calc _refine.ls_weighting_details ; Sigdel model of Konnert-Hendrickson: Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = -150.0 at beginning of refinement Afsig = 15.5, Bfsig = -50.0 at end of refinement ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _refine.details sfls:_F_calc_weight_full_matrix _refine.ls_structure_factor_coef F _refine.ls_matrix_type full _refine.ls_weighting_scheme calc _refine.ls_weighting_details 'w=1/(\s^2^(F)+0.0004F^2^)' _refine.ls_hydrogen_treatment 'refxyz except H332B noref' _refine.ls_extinction_method Zachariasen _refine.ls_extinction_coef 3514 _refine.ls_extinction_expression ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard. _refine.ls_abs_structure_details ; The absolute configuration was assigned to agree with the known chirality at C3 arising from its precursor l-leucine. ; _refine.ls_abs_structure_Flack 0 _refine.ls_number_reflns_obs 1408 _refine.ls_number_parameters 272 _refine.ls_number_restraints 0 _refine.ls_number_constraints 0 _refine.ls_R_factor_all .038 _refine.ls_R_factor_obs .034 _refine.ls_wR_factor_all .044 _refine.ls_wR_factor_obs .042 _refine.ls_goodness_of_fit_all 1.462 _refine.ls_goodness_of_fit_obs 1.515 _refine.ls_shift_over_esd_max .535 _refine.ls_shift_over_esd_mean .044 _refine.diff_density_min -.108 _refine.diff_density_max .131 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine.aniso_B[1][1] _item_description.description ; The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[1][1]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[1][2] _item_description.description ; The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[1][2]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[1][3] _item_description.description ; The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[1][3]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[2][2] _item_description.description ; The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[2][2]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[2][3] _item_description.description ; The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[2][3]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.aniso_B[3][3] _item_description.description ; The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. ; _item.name '_refine.aniso_B[3][3]' _item.category_id refine _item.mandatory_code no _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__refine.B_iso_max _item_description.description ; The maximum isotropic displacement parameter (B value) found in the coordinate set. ; _item.name '_refine.B_iso_max' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__refine.B_iso_mean _item_description.description ; The mean isotropic displacement parameter (B value) for the coordinate set. ; _item.name '_refine.B_iso_mean' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__refine.B_iso_min _item_description.description ; The minimum isotropic displacement parameter (B value) found in the coordinate set. ; _item.name '_refine.B_iso_min' _item.category_id refine _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__refine.correlation_coeff_Fo_to_Fc _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections included in the refinement ; _item.name '_refine.correlation_coeff_Fo_to_Fc' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.correlation_coeff_Fo_to_Fc_free _item_description.description ; The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - ) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections not included in the refinement (free reflections) ; _item.name '_refine.correlation_coeff_Fo_to_Fc_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc_free' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.details _item_description.description ; Description of special aspects of the refinement process. ; _item.name '_refine.details' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__refine.diff_density_max _item_description.description ; The maximum value of the electron density in the final difference Fourier map. ; _item.name '_refine.diff_density_max' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.diff_density_max_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_max_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.diff_density_max. ; _item.name '_refine.diff_density_max_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.diff_density_max' _item_related.function_code associated_value _item_type.code float _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_min _item_description.description ; The minimum value of the electron density in the final difference Fourier map. ; _item.name '_refine.diff_density_min' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.diff_density_min_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_min_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.diff_density_min. ; _item.name '_refine.diff_density_min_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.diff_density_min' _item_related.function_code associated_value _item_type.code float _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_rms _item_description.description ; The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. ; _item.name '_refine.diff_density_rms' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_diff_density_rms' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.diff_density_rms_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code electrons_per_angstroms_cubed save_ save__refine.diff_density_rms_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.diff_density_rms. ; _item.name '_refine.diff_density_rms_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.diff_density_rms' _item_related.function_code associated_value _item_type.code float _item_units.code electrons_per_angstroms_cubed save_ save__refine.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_refine.entry_id' _item.mandatory_code yes save_ save__refine.ls_abs_structure_details _item_description.description ; The nature of the absolute structure and how it was determined. For example, this may describe the Friedel pairs used. ; _item.name '_refine.ls_abs_structure_details' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__refine.ls_abs_structure_Flack _item_description.description ; The measure of absolute structure (enantiomorph or polarity) as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data name is present, is 'inapplicable', represented by '.' . For noncentrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [0.0:1.0] is correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. ; _item.name '_refine.ls_abs_structure_Flack' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_Flack' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_related.related_name '_refine.ls_abs_structure_Flack_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_abs_structure_Flack_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_abs_structure_Flack. ; _item.name '_refine.ls_abs_structure_Flack_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_abs_structure_Flack' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_abs_structure_Rogers _item_description.description ; The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< \h =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [-1.0, 1.0] is correctly interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. ; _item.name '_refine.ls_abs_structure_Rogers' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_abs_structure_Rogers' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 -1.0 -1.0 -1.0 _item_related.related_name '_refine.ls_abs_structure_Rogers_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_abs_structure_Rogers_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_abs_structure_Rogers. ; _item.name '_refine.ls_abs_structure_Rogers_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_abs_structure_Rogers' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_d_res_high _item_description.description ; The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution. ; _item.name '_refine.ls_d_res_high' _item.category_id refine _item.mandatory_code yes _item_aliases.alias_name '_refine_ls_d_res_high' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine.ls_d_res_low _item_description.description ; The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution. ; _item.name '_refine.ls_d_res_low' _item.category_id refine _item.mandatory_code yes _item_aliases.alias_name '_refine_ls_d_res_low' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine.ls_extinction_coef _item_description.description ; The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine.ls_extinction_expression and _refine.ls_extinction_method. For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-47, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. ; _item.name '_refine.ls_extinction_coef' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_coef' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refine.ls_extinction_coef_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_examples.case 3472 _item_examples.detail 'Zachariasen coefficient r* = 0.347 E04' save_ save__refine.ls_extinction_coef_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_extinction_coef. ; _item.name '_refine.ls_extinction_coef_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_extinction_coef' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_extinction_expression _item_description.description ; A description of or reference to the extinction-correction equation used to apply the data item _refine.ls_extinction_coef. This information must be sufficient to reproduce the extinction-correction factors applied to the structure factors. ; _item.name '_refine.ls_extinction_expression' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_expression' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard. ; save_ save__refine.ls_extinction_method _item_description.description ; A description of the extinction-correction method applied. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method, it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian' and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied, the multiple coefficients cannot be contained in *_extinction_coef and must be listed in _refine.details. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. ; _item.name '_refine.ls_extinction_method' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_extinction_method' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value Zachariasen _item_type.code text _item_examples.case 'B-C type 2 Gaussian isotropic' save_ save__refine.ls_goodness_of_fit_all _item_description.description ; The least-squares goodness-of-fit parameter S for all data after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of _refine.ls_restrained_S_all. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_goodness_of_fit_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_all_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_goodness_of_fit_all_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_goodness_of_fit_all. ; _item.name '_refine.ls_goodness_of_fit_all_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_all' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_goodness_of_fit_obs _item_description.description ; The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see _reflns.observed_criterion) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of _refine.ls_restrained_S_obs. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_goodness_of_fit_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_obs_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__refine.ls_goodness_of_fit_obs_esd _item_description.description ; The standard uncertainty (estimated standard deviation) of _refine.ls_goodness_of_fit_obs. ; _item.name '_refine.ls_goodness_of_fit_obs_esd' _item.category_id refine _item.mandatory_code no # _item_default.value 0.0 _item_related.related_name '_refine.ls_goodness_of_fit_obs' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_hydrogen_treatment _item_description.description ; Treatment of hydrogen atoms in the least-squares refinement. ; _item.name '_refine.ls_hydrogen_treatment' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_hydrogen_treatment' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value undef _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail refall 'refined all H-atom parameters' refxyz 'refined H-atom coordinates only' refU 'refined H-atom U's only' noref 'no refinement of H-atom parameters' constr 'H-atom parameters constrained' mixed 'some constrained, some independent' undef 'H-atom parameters not defined' save_ save__refine.ls_matrix_type _item_description.description ; Type of matrix used to accumulate the least-squares derivatives. ; _item.name '_refine.ls_matrix_type' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_matrix_type' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value full _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail full 'full' fullcycle 'full with fixed elements per cycle' atomblock 'block diagonal per atom' userblock 'user-defined blocks' diagonal 'diagonal elements only' sparse 'selected elements only' save_ save__refine.ls_number_constraints _item_description.description ; The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site.refinement_flags. A general description of constraints may appear in _refine.details. ; _item.name '_refine.ls_number_constraints' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_constraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value 0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_parameters _item_description.description ; The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. ; _item.name '_refine.ls_number_parameters' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_parameters' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_all _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ; _item.name '_refine.ls_number_reflns_all' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. ; _item.name '_refine.ls_number_reflns_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_reflns' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine.ls_number_reflns_R_free' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_reflns_R_work _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine.ls_number_reflns_R_work' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_number_restraints _item_description.description ; The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in _refine.details. ; _item.name '_refine.ls_number_restraints' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_number_restraints' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine.ls_percent_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. ; _item.name '_refine.ls_percent_reflns_obs' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_percent_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. ; _item.name '_refine.ls_percent_reflns_R_free' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_R_factor_all _item_description.description ; Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_factor_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_wR_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_R_factor_obs _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_factor_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_wR_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_R_free' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_refine.ls_wR_factor_R_free' alternate '_refine.ls_R_factor_R_free_error' associated_error _item_type.code float save_ save__refine.ls_R_factor_R_free_error _item_description.description ; The estimated error in _refine.ls_R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details. ; _item.name '_refine.ls_R_factor_R_free_error' _item.category_id refine _item.mandatory_code no _item_related.related_name '_refine.ls_R_factor_R_free' _item_related.function_code associated_value _item_type.code float save_ save__refine.ls_R_factor_R_free_error_details _item_description.description ; Special aspects of the method used to estimated the error in _refine.ls_R_factor_R_free. ; _item.name '_refine.ls_R_factor_R_free_error_details' _item.category_id refine _item.mandatory_code no _item_type.code text save_ save__refine.ls_R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_R_work' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_wR_factor_R_work' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_R_Fsqd_factor_obs _item_description.description ; Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the squares of the observed and calculated structure-factor amplitudes. sum|F~obs~^2^ - F~calc~^2^| R(Fsqd) = --------------------------- sum|F~obs~^2^| F~obs~^2^ = squares of the observed structure-factor amplitudes F~calc~^2^ = squares of the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine.ls_R_Fsqd_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_Fsqd_factor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_R_I_factor_obs _item_description.description ; Residual factor R(I) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum|I~obs~ - I~calc~| R(I) = --------------------- sum|I~obs~| I~obs~ = the net observed intensities I~calc~ = the net calculated intensities sum is taken over the specified reflections ; _item.name '_refine.ls_R_I_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_R_I_factor' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_redundancy_reflns_all _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine.ls_redundancy_reflns_all' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_redundancy_reflns_obs _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine.ls_redundancy_reflns_obs' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.ls_restrained_S_all _item_description.description ; The least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_all. ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) N~restr~ = the number of restraints (see _refine.ls_number_restraints) N~param~ = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflections sumr is taken over the restraints ; _item.name '_refine.ls_restrained_S_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_restrained_S_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_restrained_S_obs _item_description.description ; The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see _reflns.observed_criterion) after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_obs. ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see _refine.ls_structure_factor_coef) Y~calc~ = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) N~restr~ = the number of restraints (see _refine.ls_number_restraints) N~param~ = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflections sumr is taken over the restraints ; _item.name '_refine.ls_restrained_S_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_restrained_S_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_shift_over_esd_max _item_description.description ; The largest ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). ; _item.name '_refine.ls_shift_over_esd_max' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_shift/esd_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_shift_over_esd_mean _item_description.description ; The average ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). ; _item.name '_refine.ls_shift_over_esd_mean' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_shift/esd_mean' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.ls_structure_factor_coef _item_description.description ; Structure-factor coefficient |F|, F^2^ or I used in the least- squares refinement process. ; _item.name '_refine.ls_structure_factor_coef' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_structure_factor_coef' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value F _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail F 'structure-factor magnitude' Fsqd 'structure factor squared' Inet 'net intensity' save_ save__refine.ls_weighting_details _item_description.description ; A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of _refine.ls_weighting_scheme is specified as 'calc'. ; _item.name '_refine.ls_weighting_details' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_weighting_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case ; Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. ; save_ save__refine.ls_weighting_scheme _item_description.description ; The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see _refine.ls_weighting_details for a preferred approach). ; _item.name '_refine.ls_weighting_scheme' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_weighting_scheme' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value sigma _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sigma 'based on measured e.s.d.'s' unit 'unit or no weights applied' calc 'calculated weights applied' save_ save__refine.ls_wR_factor_all _item_description.description ; Weighted residual factor wR for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_all' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_wR_factor_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_wR_factor_obs _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_obs' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine_ls_wR_factor_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_wR_factor_R_free _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_R_free' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_R_free' _item_related.function_code alternate _item_type.code float save_ save__refine.ls_wR_factor_R_work _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine.ls_wR_factor_R_work' _item.category_id refine _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine.ls_R_factor_R_work' _item_related.function_code alternate _item_type.code float save_ save__refine.occupancy_max _item_description.description ; The maximum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_max' _item.category_id refine _item.mandatory_code no # _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.occupancy_min _item_description.description ; The minimum value for occupancy found in the coordinate set. ; _item.name '_refine.occupancy_min' _item.category_id refine _item.mandatory_code no # _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine.overall_SU_B _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum-likelihood residual. The overall standard uncertainty (sigma~B~)^2 gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma~B~)^2 = 8 ---------------------------------------------- sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^4} SUM_AS = (sigma_A)^2/Sigma^2 N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2] E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_B' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_B' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_SU_ML _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N_a (sigma~X~)^2 = ----------------------------------------------------- 8 pi^2 sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^2} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon [1-{sigma_A)^2] E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector epsilon = multiplicity of the diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_ML' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_ML' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_SU_R_Cruickshank_DPI _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3) (N_o-N_p) N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_value = conventional crystallographic R value D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_R_Cruickshank_DPI' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_SU_R_free _item_description.description ; The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value. The overall standard uncertainty gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3) N_o N_a = number of atoms N_o = number of reflections included in refinement R_free = conventional free crystallographic R value calculated using reflections not included in refinement D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html ; _item.name '_refine.overall_SU_R_free' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_Overall_ESU_Rfree' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_FOM_free_R_set _item_description.description ; Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel functions of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2] sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. ; _item.name '_refine.overall_FOM_free_R_set' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_FOM_free_Rset' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.overall_FOM_work_R_set _item_description.description ; Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel functions of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2] sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. ; _item.name '_refine.overall_FOM_work_R_set' _item.category_id refine _item.mandatory_code no _item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refine.solvent_model_details _item_description.description ; Special aspects of the solvent model used during refinement. ; _item.name '_refine.solvent_model_details' _item.category_id refine _item.mandatory_code no _item_type.code text save_ save__refine.solvent_model_param_bsol _item_description.description ; The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms. This is one of the two parameters (the other is _refine.solvent_model_param_ksol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. ; _item.name '_refine.solvent_model_param_bsol' _item.category_id refine _item.mandatory_code no _item_type.code float save_ save__refine.solvent_model_param_ksol _item_description.description ; The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute. This is one of the two parameters (the other is _refine.solvent_model_param_bsol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. ; _item.name '_refine.solvent_model_param_ksol' _item.category_id refine _item.mandatory_code no _item_type.code float save_ #################### ## REFINE_ANALYZE ## #################### save_refine_analyze _category.description ; Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names. ; _category.id refine_analyze _category.mandatory_code no _category_key.name '_refine_analyze.entry_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_analyze.entry_id _refine_analyze.Luzzati_coordinate_error_obs _refine_analyze.Luzzati_d_res_low_obs 5HVP 0.056 2.51 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_analyze.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_refine_analyze.entry_id' _item.category_id refine_analyze _item.mandatory_code yes save_ save__refine_analyze.Luzzati_coordinate_error_free _item_description.description ; The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_coordinate_error_free' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_coordinate_error_obs _item_description.description ; The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_coordinate_error_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_d_res_low_free _item_description.description ; The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_d_res_low_free' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_d_res_low_obs _item_description.description ; The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_d_res_low_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_sigma_a_free _item_description.description ; The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_free_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_free' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_sigma_a_free_details _item_description.description ; Details of the estimation of sigma~a~ for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_free_details' _item.category_id refine_analyze _item.mandatory_code no _item_type.code text save_ save__refine_analyze.Luzzati_sigma_a_obs _item_description.description ; The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigma~a~ can be specified in _refine_analyze.Luzzati_sigma_a_obs_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_obs' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ save__refine_analyze.Luzzati_sigma_a_obs_details _item_description.description ; Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. ; _item.name '_refine_analyze.Luzzati_sigma_a_obs_details' _item.category_id refine_analyze _item.mandatory_code no _item_type.code text save_ save__refine_analyze.number_disordered_residues _item_description.description ; The number of discretely disordered residues in the refined model. ; _item.name '_refine_analyze.number_disordered_residues' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float save_ save__refine_analyze.occupancy_sum_hydrogen _item_description.description ; The sum of the occupancies of the hydrogen atoms in the refined model. ; _item.name '_refine_analyze.occupancy_sum_hydrogen' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float save_ save__refine_analyze.occupancy_sum_non_hydrogen _item_description.description ; The sum of the occupancies of the non-hydrogen atoms in the refined model. ; _item.name '_refine_analyze.occupancy_sum_non_hydrogen' _item.category_id refine_analyze _item.mandatory_code no _item_type.code float save_ save__refine_analyze.RG_d_res_high _item_description.description ; The value of the high-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in _refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_d_res_high' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_high' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_analyze.RG_d_res_low _item_description.description ; The value of the low-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in _refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_d_res_low' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_low' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_analyze.RG_free _item_description.description ; The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_free' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_free' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_analyze.RG_work _item_description.description ; The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low and for those reflections included in the working set when a free R set of reflections is omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. ; _item.name '_refine_analyze.RG_work' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_work' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_analyze.RG_free_work_ratio _item_description.description ; The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in the data and the model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement, the ratio of RGfree to RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters according to sqrt[(f + m) / (f - m) ] where f = the number of included structure amplitudes and target distances, and m = the number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in the refinement, the RG ratio requires a term for the contribution to the minimized residual at convergence, D~restr~, due to those restraints: D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i] where r is the number of geometrical, displacement-parameter and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ] There is no data name for the expected value of RGfree/RGwork yet. Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557. ; _item.name '_refine_analyze.RG_free_work_ratio' _item.category_id refine_analyze _item.mandatory_code no _item_aliases.alias_name '_refine_analyze.ebi_RG_work_free_ratio' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################## ## REFINE_B_ISO ## ################## save_refine_B_iso _category.description ; Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement. ; _category.id refine_B_iso _category.mandatory_code no _category_key.name '_refine_B_iso.class' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_B_iso.class _refine_B_iso.treatment 'protein' isotropic 'solvent' isotropic 'inhibitor' isotropic ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_B_iso.class _item_description.description ; A class of atoms treated similarly for isotropic B-factor (displacement-parameter) refinement. ; _item.name '_refine_B_iso.class' _item.category_id refine_B_iso _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone' save_ save__refine_B_iso.details _item_description.description ; A description of special aspects of the isotropic B-factor (displacement-parameter) refinement for the class of atoms described in _refine_B_iso.class. ; _item.name '_refine_B_iso.details' _item.category_id refine_B_iso _item.mandatory_code no _item_type.code text _item_examples.case ; The temperature factors of atoms in the side chain of Arg 92 were held fixed due to unstable behavior in refinement. ; save_ save__refine_B_iso.treatment _item_description.description ; The treatment of isotropic B-factor (displacement-parameter) refinement for a class of atoms defined in _refine_B_iso.class. ; _item.name '_refine_B_iso.treatment' _item.category_id refine_B_iso _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value fixed isotropic anisotropic save_ save__refine_B_iso.value _item_description.description ; The value of the isotropic B factor (displacement parameter) assigned to a class of atoms defined in _refine_B_iso.class. Meaningful only for atoms with fixed isotropic B factors. ; _item.name '_refine_B_iso.value' _item.category_id refine_B_iso _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ ############################### ## REFINE_FUNCTION_MINIMIZED ## ############################### save_refine_funct_minimized _category.description ; Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement. ; _category.id refine_funct_minimized _category.mandatory_code no _category_key.name '_refine_funct_minimized.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. ; ; loop_ _refine_funct_minimized.type _refine_funct_minimized.number_terms _refine_funct_minimized.residual 'sum(W*Delta(Amplitude)^2' 3009 1621.3 'sum(W*Delta(Plane+Rigid)^2' 85 56.68 'sum(W*Delta(Distance)^2' 1219 163.59 'sum(W*Delta(U-tempfactors)^2' 1192 69.338 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_funct_minimized.number_terms _item_description.description ; The number of observations in this term. For example, if the term is a residual of the X-ray intensities, this item would contain the number of reflections used in the refinement. ; _item.name '_refine_funct_minimized.number_terms' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.NumTerms' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_funct_minimized.residual _item_description.description ; The residual for this term of the function that was minimized during the refinement. ; _item.name '_refine_funct_minimized.residual' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.Residual' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_funct_minimized.type _item_description.description ; The type of the function being minimized. ; _item.name '_refine_funct_minimized.type' _item.category_id refine_funct_minimized _item.mandatory_code yes _item_aliases.alias_name '_ebi_refine_funct_minimized.type' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code line save_ save__refine_funct_minimized.weight _item_description.description ; The weight applied to this term of the function that was minimized during the refinement. ; _item.name '_refine_funct_minimized.weight' _item.category_id refine_funct_minimized _item.mandatory_code no _item_aliases.alias_name '_ebi_refine_funct_minimized.weight' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ ################# ## REFINE_HIST ## ################# save_refine_hist _category.description ; Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics. ; _category.id refine_hist _category.mandatory_code no _category_key.name '_refine_hist.cycle_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. ; ; _refine_hist.cycle_id C134 _refine_hist.d_res_high 1.85 _refine_hist.d_res_low 20.0 _refine_hist.number_atoms_solvent 217 _refine_hist.number_atoms_total 808 _refine_hist.number_reflns_all 6174 _refine_hist.number_reflns_obs 4886 _refine_hist.number_reflns_R_free 476 _refine_hist.number_reflns_R_work 4410 _refine_hist.R_factor_all .265 _refine_hist.R_factor_obs .195 _refine_hist.R_factor_R_free .274 _refine_hist.R_factor_R_work .160 _refine_hist.details ; Add majority of solvent molecules. B factors refined by group. Continued to remove misplaced water molecules. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_hist.cycle_id _item_description.description ; The value of _refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_refine_hist.cycle_id' _item.category_id refine_hist _item.mandatory_code yes _item_type.code code save_ save__refine_hist.details _item_description.description ; A description of special aspects of this cycle of the refinement process. ; _item.name '_refine_hist.details' _item.category_id refine_hist _item.mandatory_code no _item_type.code text _item_examples.case ; Residues 13-17 fit and added to model; substantial rebuilding of loop containing residues 43-48; addition of first atoms to solvent model; ten cycles of Prolsq refinement. ; save_ save__refine_hist.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution. ; _item.name '_refine_hist.d_res_high' _item.category_id refine_hist _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_hist.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution. ; _item.name '_refine_hist.d_res_low' _item.category_id refine_hist _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_hist.number_atoms_solvent _item_description.description ; The number of solvent atoms that were included in the model at this cycle of the refinement. ; _item.name '_refine_hist.number_atoms_solvent' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_atoms_total _item_description.description ; The total number of atoms that were included in the model at this cycle of the refinement. ; _item.name '_refine_hist.number_atoms_total' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_all _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low. ; _item.name '_refine_hist.number_reflns_all' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion. ; _item.name '_refine_hist.number_reflns_obs' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_hist.number_reflns_R_free' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.number_reflns_R_work _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_hist.number_reflns_R_work' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_hist.R_factor_all _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_all' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_hist.R_factor_obs _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_obs' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_hist.R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_R_free' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_hist.R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_hist.R_factor_R_work' _item.category_id refine_hist _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ##################### ## REFINE_LS_RESTR ## ##################### save_refine_ls_restr _category.description ; Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement. ; _category.id refine_ls_restr _category.mandatory_code no _category_key.name '_refine_ls_restr.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal_target _refine_ls_restr.dev_ideal _refine_ls_restr.number _refine_ls_restr.criterion _refine_ls_restr.rejects 'bond_d' 0.020 0.018 1654 '> 2\s' 22 'angle_d' 0.030 0.038 2246 '> 2\s' 139 'planar_d' 0.040 0.043 498 '> 2\s' 21 'planar' 0.020 0.015 270 '> 2\s' 1 'chiral' 0.150 0.177 278 '> 2\s' 2 'singtor_nbd' 0.500 0.216 582 '> 2\s' 0 'multtor_nbd' 0.500 0.207 419 '> 2\s' 0 'xyhbond_nbd' 0.500 0.245 149 '> 2\s' 0 'planar_tor' 3.0 2.6 203 '> 2\s' 9 'staggered_tor' 15.0 17.4 298 '> 2\s' 31 'orthonormal_tor' 20.0 18.1 12 '> 2\s' 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr.criterion _item_description.description ; A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement. ; _item.name '_refine_ls_restr.criterion' _item.category_id refine_ls_restr _item.mandatory_code no _item_type.code text _item_examples.case '> 3\s' save_ save__refine_ls_restr.dev_ideal _item_description.description ; For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (r.m.s.) from ideal values in the current model. ; _item.name '_refine_ls_restr.dev_ideal' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_ls_restr.dev_ideal_target _item_description.description ; For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. ; _item.name '_refine_ls_restr.dev_ideal_target' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refine_ls_restr.number _item_description.description ; The number of parameters of this type subjected to restraint in least-squares refinement. ; _item.name '_refine_ls_restr.number' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_restr.rejects _item_description.description ; The number of parameters of this type that deviate from ideal values by more than the amount defined in _refine_ls_restr.criterion in the model obtained by restrained least-squares refinement. ; _item.name '_refine_ls_restr.rejects' _item.category_id refine_ls_restr _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_restr.type _item_description.description ; The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs change, these data values are given as examples, not as an enumeration list. Computer programs that convert a data block to a refinement table will expect the exact form of the data values given here to be used. ; loop_ _item.name _item.category_id _item.mandatory_code '_refine_ls_restr.type' refine_ls_restr yes '_refine_ls_restr_type.type' refine_ls_restr_type yes loop_ _item_linked.child_name _item_linked.parent_name '_refine_ls_restr_type.type' '_refine_ls_restr.type' _item_type.code line loop_ _item_examples.case _item_examples.detail 'p_bond_d' 'bond distance' 'p_angle_d' 'bond angle expressed as a distance' 'p_planar_d' 'planar 1,4 distance' 'p_xhbond_d' 'X-H bond distance' 'p_xhangle_d' 'X-H bond angle expressed as a distance' 'p_hydrog_d' 'hydrogen distance' 'p_special_d' 'special distance' 'p_planar' 'planes' 'p_chiral' 'chiral centres' 'p_singtor_nbd' 'single-torsion non-bonded contact' 'p_multtor_nbd' 'multiple-torsion non-bonded contact' 'p_xyhbond_nbd' 'possible (X...Y) hydrogen bond' 'p_xhyhbond_nbd' 'possible (X-H...Y) hydrogen bond' 'p_special_tor' 'special torsion angle' 'p_planar_tor' 'planar torsion angle' 'p_staggered_tor' 'staggered torsion angle' 'p_orthonormal_tor' 'orthonormal torsion angle' 'p_mcbond_it' 'main-chain bond isotropic displacement parameter' 'p_mcangle_it' 'main-chain angle isotropic displacement parameter' 'p_scbond_it' 'side-chain bond isotropic displacement parameter' 'p_scangle_it' 'side-chain angle isotropic displacement parameter' 'p_xhbond_it' 'X-H bond isotropic displacement parameter' 'p_xhangle_it' 'X-H angle isotropic displacement parameter' 'p_special_it' 'special isotropic displacement parameter' 'RESTRAIN_Distances < 2.12' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 Angstroms. ; 'RESTRAIN_Distances 2.12 < D < 2.625' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 Angstroms. ; 'RESTRAIN_Distances > 2.625' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 Angstroms. ; 'RESTRAIN_Peptide Planes' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. ; 'RESTRAIN_Ring and other planes' ; The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. ; 'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' . 'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' . save_ save__refine_ls_restr.weight _item_description.description ; The weighting value applied to this type of restraint in the least-squares refinement. ; _item.name '_refine_ls_restr.weight' _item.category_id refine_ls_restr _item.mandatory_code no _item_type.code float save_ ######################### ## REFINE_LS_RESTR_NCS ## ######################### save_refine_ls_restr_ncs _category.description ; Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains. ; _category.id refine_ls_restr_ncs _category.mandatory_code no _category_key.name '_refine_ls_restr_ncs.dom_id' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; _refine_ls_restr_ncs.dom_id d2 _refine_ls_restr_ncs.weight_position 300.0 _refine_ls_restr_ncs.weight_B_iso 2.0 _refine_ls_restr_ncs.rms_dev_position 0.09 _refine_ls_restr_ncs.rms_dev_B_iso 0.16 _refine_ls_restr_ncs.ncs_model_details ; NCS restraint for pseudo-twofold symmetry between domains d1 and d2. Position weight coefficient given in Kcal/(mol \%A^2^) and isotropic B weight coefficient given in \%A^2^. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr_ncs.dom_id _item_description.description ; This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_refine_ls_restr_ncs.dom_id' _item.category_id refine_ls_restr_ncs _item.mandatory_code yes _item_type.code code save_ save__refine_ls_restr_ncs.ncs_model_details _item_description.description ; Special aspects of the manner in which noncrystallographic restraints were applied to atomic parameters in the domain specified by _refine_ls_restr_ncs.dom_id and equivalent atomic parameters in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.ncs_model_details' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code text save_ save__refine_ls_restr_ncs.rms_dev_B_iso _item_description.description ; The root-mean-square deviation in equivalent isotropic displacement parameters in the domain specified by _refine_ls_restr_ncs.dom_id and in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.rms_dev_B_iso' _item.category_id refine_ls_restr_ncs _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms_squared save_ save__refine_ls_restr_ncs.rms_dev_position _item_description.description ; The root-mean-square deviation in equivalent atom positions in the domain specified by _refine_ls_restr_ncs.dom_id and in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.rms_dev_position' _item.category_id refine_ls_restr_ncs _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_ncs.weight_B_iso _item_description.description ; The value of the weighting coefficient used in noncrystallographic symmetry restraint of isotropic displacement parameters in the domain specified by _refine_ls_restr_ncs.dom_id to equivalent isotropic displacement parameters in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.weight_B_iso' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code float save_ save__refine_ls_restr_ncs.weight_position _item_description.description ; The value of the weighting coefficient used in noncrystallographic symmetry restraint of atom positions in the domain specified by _refine_ls_restr_ncs.dom_id to equivalent atom positions in the domains against which it was restrained. ; _item.name '_refine_ls_restr_ncs.weight_position' _item.category_id refine_ls_restr_ncs _item.mandatory_code no _item_type.code float save_ ########################## ## REFINE_LS_RESTR_TYPE ## ########################## save_refine_ls_restr_type _category.description ; Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement. ; _category.id refine_ls_restr_type _category.mandatory_code no _category_key.name '_refine_ls_restr_type.type' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. ; ; loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target 'RESTRAIN_Distances < 2.12' 509 0.005 0.022 'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037 'RESTRAIN_Distances > 2.625' 39 0.034 0.043 'RESTRAIN_Peptide Planes' 59 0.002 0.010 'RESTRAIN_Ring and other planes' 26 0.014 0.010 'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' 212 0.106 . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' 288 0.101 . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' 6 0.077 . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' 10 0.114 . 'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' 215 0.119 . 'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' 461 0.106 . loop_ _refine_ls_restr_type.type _refine_ls_restr_type.distance_cutoff_low _refine_ls_restr_type.distance_cutoff_high 'RESTRAIN_Distances < 2.12' . 2.12 'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625 'RESTRAIN_Distances > 2.625' 2.625 . 'RESTRAIN_Peptide Planes' . . 'RESTRAIN_Ring and other planes' . . 'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' 1.2 1.4 'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' 1.4 1.6 'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' 1.8 2.0 'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' 2.0 2.2 'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' 2.2 2.4 'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' 2.4 . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_restr_type.distance_cutoff_high _item_description.description ; The upper limit in angstroms of the distance range applied to the current restraint type. ; _item.name '_refine_ls_restr_type.distance_cutoff_high' _item.category_id refine_ls_restr_type _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_type.distance_cutoff_low _item_description.description ; The lower limit in angstroms of the distance range applied to the current restraint type. ; _item.name '_refine_ls_restr_type.distance_cutoff_low' _item.category_id refine_ls_restr_type _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_restr_type.type _item_description.description ; This data item is a pointer to _refine_ls_restr.type in the REFINE_LS_RESTR category. ; _item.name '_refine_ls_restr_type.type' _item.category_id refine_ls_restr_type _item.mandatory_code yes _item_type.code line save_ ##################### ## REFINE_LS_SHELL ## ##################### save_refine_ls_shell _category.description ; Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution. ; _category.id refine_ls_shell _category.mandatory_code no loop_ _category_key.name '_refine_ls_shell.d_res_low' '_refine_ls_shell.d_res_high' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high _refine_ls_shell.number_reflns_obs _refine_ls_shell.R_factor_obs 8.00 4.51 1226 0.196 4.51 3.48 1679 0.146 3.48 2.94 2014 0.160 2.94 2.59 2147 0.182 2.59 2.34 2127 0.193 2.34 2.15 2061 0.203 2.15 2.00 1647 0.188 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_shell.d_res_high _item_description.description ; The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. ; _item.name '_refine_ls_shell.d_res_high' _item.category_id refine_ls_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_shell.d_res_low _item_description.description ; The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. ; _item.name '_refine_ls_shell.d_res_low' _item.category_id refine_ls_shell _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refine_ls_shell.number_reflns_all _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ; _item.name '_refine_ls_shell.number_reflns_all' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.number_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ; _item.name '_refine_ls_shell.number_reflns_obs' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.number_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_ls_shell.number_reflns_R_free' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.number_reflns_R_work _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ; _item.name '_refine_ls_shell.number_reflns_R_work' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__refine_ls_shell.percent_reflns_obs _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. ; _item.name '_refine_ls_shell.percent_reflns_obs' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.percent_reflns_R_free _item_description.description ; The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the reflection limits. ; _item.name '_refine_ls_shell.percent_reflns_R_free' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.R_factor_all _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_all' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.wR_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.R_factor_obs _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_obs' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.wR_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.R_factor_R_free _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_R_free' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_refine_ls_shell.wR_factor_R_free' alternate '_refine_ls_shell.R_factor_R_free_error' associated_error _item_type.code float save_ save__refine_ls_shell.R_factor_R_free_error _item_description.description ; The estimated error in _refine_ls_shell.R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details. ; _item.name '_refine_ls_shell.R_factor_R_free_error' _item.category_id refine_ls_shell _item.mandatory_code no _item_related.related_name '_refine_ls_shell.R_factor_R_free' _item_related.function_code associated_value _item_type.code float save_ save__refine_ls_shell.R_factor_R_work _item_description.description ; Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections ; _item.name '_refine_ls_shell.R_factor_R_work' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.wR_factor_R_work' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.redundancy_reflns_all _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine_ls_shell.redundancy_reflns_all' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.redundancy_reflns_obs _item_description.description ; The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits. ; _item.name '_refine_ls_shell.redundancy_reflns_obs' _item.category_id refine_ls_shell _item.mandatory_code no _item_type.code float save_ save__refine_ls_shell.wR_factor_all _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_all' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_all' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.wR_factor_obs _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_obs' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_obs' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.wR_factor_R_free _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_R_free' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_R_free' _item_related.function_code alternate _item_type.code float save_ save__refine_ls_shell.wR_factor_R_work _item_description.description ; Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections ; _item.name '_refine_ls_shell.wR_factor_R_work' _item.category_id refine_ls_shell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_refine_ls_shell.R_factor_R_work' _item_related.function_code alternate _item_type.code float save_ ###################### ## REFINE_OCCUPANCY ## ###################### save_refine_occupancy _category.description ; Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement. ; _category.id refine_occupancy _category.mandatory_code no _category_key.name '_refine_occupancy.class' loop_ _category_group.id 'inclusive_group' 'refine_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.value _refine_occupancy.details 'protein' fix 1.00 . 'solvent' fix 1.00 . 'inhibitor orientation 1' fix 0.65 . 'inhibitor orientation 2' fix 0.35 ; The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_occupancy.class _item_description.description ; The class of atoms treated similarly for occupancy refinement. ; _item.name '_refine_occupancy.class' _item.category_id refine_occupancy _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'all' 'protein' 'solvent' 'sugar-phosphate backbone' save_ save__refine_occupancy.details _item_description.description ; A description of special aspects of the occupancy refinement for a class of atoms described in _refine_occupancy.class. ; _item.name '_refine_occupancy.details' _item.category_id refine_occupancy _item.mandatory_code no _item_type.code text _item_examples.case ; The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. ; save_ save__refine_occupancy.treatment _item_description.description ; The treatment of occupancies for a class of atoms described in _refine_occupancy.class. ; _item.name '_refine_occupancy.treatment' _item.category_id refine_occupancy _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail fix 'fixed' ref 'refined' save_ save__refine_occupancy.value _item_description.description ; The value of occupancy assigned to a class of atoms defined in _refine_occupancy.class. Meaningful only for atoms with fixed occupancy. ; _item.name '_refine_occupancy.value' _item.category_id refine_occupancy _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float loop_ _item_examples.case 1.0 0.41 save_ ########### ## REFLN ## ########### save_refln _category.description ; Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _category.id refln _category.mandatory_code no loop_ _category_key.name '_refln.index_h' '_refln.index_k' '_refln.index_l' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [Acta Cryst. (1993), C49, 1352-1354]. ; ; loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_squared_calc _refln.F_squared_meas _refln.F_squared_sigma _refln.status 2 0 0 85.57 58.90 1.45 o 3 0 0 15718.18 15631.06 30.40 o 4 0 0 55613.11 49840.09 61.86 o 5 0 0 246.85 241.86 10.02 o 6 0 0 82.16 69.97 1.93 o 7 0 0 1133.62 947.79 11.78 o 8 0 0 2558.04 2453.33 20.44 o 9 0 0 283.88 393.66 7.79 o 10 0 0 283.70 171.98 4.26 o ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refln.A_calc _item_description.description ; The calculated value of structure-factor component A in electrons. A = |F|cos(phase) ; _item.name '_refln.A_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_A_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.A_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.A_calc_au _item_description.description ; The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase) ; _item.name '_refln.A_calc_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.A_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.A_meas _item_description.description ; The measured value of structure-factor component A in electrons. A = |F|cos(phase) ; _item.name '_refln.A_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_A_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.A_meas_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.A_meas_au _item_description.description ; The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase) ; _item.name '_refln.A_meas_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.A_meas' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.B_calc _item_description.description ; The calculated value of structure-factor component B in electrons. B = |F|sin(phase) ; _item.name '_refln.B_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_B_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.B_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.B_calc_au _item_description.description ; The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase) ; _item.name '_refln.B_calc_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.B_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.B_meas _item_description.description ; The measured value of structure-factor component B in electrons. B = |F|sin(phase) ; _item.name '_refln.B_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_B_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.B_meas_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.B_meas_au _item_description.description ; The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase) ; _item.name '_refln.B_meas_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.B_meas' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_refln.crystal_id' _item.mandatory_code yes _item_aliases.alias_name '_refln_crystal_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__refln.F_calc _item_description.description ; The calculated value of the structure factor in electrons. ; _item.name '_refln.F_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_related.related_name '_refln.F_calc_au' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.F_calc_au _item_description.description ; The calculated value of the structure factor in arbitrary units. ; _item.name '_refln.F_calc_au' _item.category_id refln _item.mandatory_code no _item_related.related_name '_refln.F_calc' _item_related.function_code conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.F_meas _item_description.description ; The measured value of the structure factor in electrons. ; _item.name '_refln.F_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_refln.F_meas_sigma' associated_esd '_refln.F_meas_au' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code electrons save_ save__refln.F_meas_au _item_description.description ; The measured value of the structure factor in arbitrary units. ; _item.name '_refln.F_meas_au' _item.category_id refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_refln.F_meas_sigma_au' associated_esd '_refln.F_meas' conversion_arbitrary _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln.F_meas_sigma _item_description.description ; The standard uncertainty (estimated standard deviation) of _refln.F_meas in electrons. ; _item.name '_refln.F_meas_sigma' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_refln.F_meas' associated_value '_refln.F_meas_sigma_au' conversion_arbitrary _item_type.code float _item_units.code electrons save_ save__refln.F_meas_sigma_au _item_description.description ; The standard uncertainty (estimated standard deviation) of _refln.F_meas_au in arbitrary units. ; _item.name '_refln.F_meas_sigma_au' _item.category_id refln _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_refln.F_meas_au' associated_value '_refln.F_meas_sigma' conversion_arbitrary _item_type.code float _item_units.code arbitrary save_ save__refln.F_squared_calc _item_description.description ; The calculated value of the squared structure factor in electrons squared. ; _item.name '_refln.F_squared_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code electrons_squared save_ save__refln.F_squared_meas _item_description.description ; The measured value of the squared structure factor in electrons squared. ; _item.name '_refln.F_squared_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code electrons_squared save_ save__refln.F_squared_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared. ; _item.name '_refln.F_squared_sigma' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_F_squared_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code electrons_squared save_ save__refln.fom _item_description.description ; The figure of merit m for this reflection. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct int is taken over the range alpha = 0 to 2 pi. ; _item.name '_refln.fom' _item.category_id refln _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__refln.index_h _item_description.description ; Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_h' _item.category_id refln _item.mandatory_code yes _item_aliases.alias_name '_refln_index_h' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_refln.index_k' '_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln.index_k _item_description.description ; Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_k' _item.category_id refln _item.mandatory_code yes _item_aliases.alias_name '_refln_index_k' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_refln.index_h' '_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln.index_l _item_description.description ; Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln.index_l' _item.category_id refln _item.mandatory_code yes _item_aliases.alias_name '_refln_index_l' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_refln.index_h' '_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__refln.intensity_calc _item_description.description ; The calculated value of the intensity in the same units as _refln.intensity_meas. ; _item.name '_refln.intensity_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__refln.intensity_meas _item_description.description ; The measured value of the intensity. ; _item.name '_refln.intensity_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__refln.intensity_sigma _item_description.description ; The standard uncertainty (derived from measurement) of the intensity in the same units as _refln.intensity_meas. ; _item.name '_refln.intensity_sigma' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_intensity_sigma' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ #save__refln.mean_path_length_tbar # _item_description.description #; Mean path length in millimetres through the crystal for this # reflection. #; # _item.name '_refln.mean_path_length_tbar' # _item.category_id refln # _item.mandatory_code no # _item_aliases.alias_name '_refln_mean_path_length_tbar' # _item_aliases.dictionary cif_core.dic # _item_aliases.version 2.0.1 # _item_type.code float # _item_units.code millimetres # save_ save__refln.status _item_description.description ; Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. ; _item.name '_refln.status' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_observed_status' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 # _item_default.value o _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail o ; satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, observed by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable ; < ; satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, unobserved by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine.ls_d_res_high' l 'does not satisfy _refine.ls_d_res_low' f ; satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, observed by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable, excluded from refinement so as to be included in the calculation of a 'free' R factor ; save_ save__refln.phase_calc _item_description.description ; The calculated structure-factor phase in degrees. ; _item.name '_refln.phase_calc' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_phase_calc' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__refln.phase_meas _item_description.description ; The measured structure-factor phase in degrees. ; _item.name '_refln.phase_meas' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_phase_meas' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_units.code degrees save_ save__refln.refinement_status _item_description.description ; Status of a reflection in the structure-refinement process. ; _item.name '_refln.refinement_status' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_refinement_status' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value incl _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail incl 'included in ls process' excl 'excluded from ls process' extn 'excluded due to extinction' save_ save__refln.scale_group_code _item_description.description ; This data item is a pointer to _reflns_scale.group_code in the REFLNS_SCALE category. ; _item.name '_refln.scale_group_code' _item.mandatory_code yes _item_aliases.alias_name '_refln_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__refln.sint_over_lambda _item_description.description ; The (sin theta)/lambda value in reciprocal angstroms for this reflection. ; _item.name '_refln.sint_over_lambda' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_sint/lambda' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code reciprocal_angstroms save_ save__refln.symmetry_epsilon _item_description.description ; The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. ; _item.name '_refln.symmetry_epsilon' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_symmetry_epsilon' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 48 48 48 1 1 1 _item_type.code int save_ save__refln.symmetry_multiplicity _item_description.description ; The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship. ; _item.name '_refln.symmetry_multiplicity' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_symmetry_multiplicity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum 48 48 48 1 1 1 _item_type.code int save_ save__refln.wavelength _item_description.description ; The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. ; _item.name '_refln.wavelength' _item.category_id refln _item.mandatory_code no _item_aliases.alias_name '_refln_wavelength' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__refln.wavelength_id _item_description.description ; This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category. ; _item.name '_refln.wavelength_id' _item.mandatory_code yes _item_aliases.alias_name '_refln_wavelength_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ ################### ## REFLN_SYS_ABS ## ################### save_refln_sys_abs _category.description ; Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group. ; _category.id refln_sys_abs _category.mandatory_code no loop_ _category_key.name '_refln_sys_abs.index_h' '_refln_sys_abs.index_k' '_refln_sys_abs.index_l' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - hypothetical example. ; ; loop_ _refln_sys_abs.index_h _refln_sys_abs.index_k _refln_sys_abs.index_l _refln_sys_abs.I _refln_sys_abs.sigmaI _refln_sys_abs.I_over_sigmaI 0 3 0 28.32 22.95 1.23 0 5 0 14.11 16.38 0.86 0 7 0 114.81 20.22 5.67 0 9 0 32.99 24.51 1.35 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refln_sys_abs.I _item_description.description ; The measured value of the intensity in arbitrary units. ; _item.name '_refln_sys_abs.I' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.I' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_related.related_name _item_related.function_code '_refln_sys_abs.sigmaI' associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code arbitrary save_ save__refln_sys_abs.I_over_sigmaI _item_description.description ; The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent. ; _item.name '_refln_sys_abs.I_over_sigmaI' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.I_over_sigma' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 _item_type.code float save_ save__refln_sys_abs.index_h _item_description.description ; Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_h' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.h' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_k' '_refln_sys_abs.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.index_k _item_description.description ; Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_k' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.k' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_h' '_refln_sys_abs.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.index_l _item_description.description ; Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. ; _item.name '_refln_sys_abs.index_l' _item.category_id refln_sys_abs _item.mandatory_code yes _item_aliases.alias_name '_ebi_refln_sys_abs.l' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_dependent.dependent_name '_refln_sys_abs.index_h' '_refln_sys_abs.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__refln_sys_abs.sigmaI _item_description.description ; The standard uncertainty (estimated standard deviation) of _refln_sys_abs.I in arbitrary units. ; _item.name '_refln_sys_abs.sigmaI' _item.category_id refln_sys_abs _item.mandatory_code no _item_aliases.alias_name '_ebi_refln_sys_abs.sigmaI' _item_aliases.dictionary ebi_extensions _item_aliases.version 1.0 loop_ _item_related.related_name _item_related.function_code '_refln_sys_abs.I' associated_value _item_type.code float _item_units.code arbitrary save_ ############ ## REFLNS ## ############ save_reflns _category.description ; Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. ; _category.id reflns _category.mandatory_code no _category_key.name '_reflns.entry_id' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _reflns.entry_id '5HVP' _reflns.data_reduction_method ; Xengen program scalei. Anomalous pairs were merged. Scaling proceeded in several passes, beginning with 1-parameter fit and ending with 3-parameter fit. ; _reflns.data_reduction_details ; Merging and scaling based on only those reflections with I > \s(I). ; _reflns.d_resolution_high 2.00 _reflns.d_resolution_low 8.00 _reflns.limit_h_max 22 _reflns.limit_h_min 0 _reflns.limit_k_max 46 _reflns.limit_k_min 0 _reflns.limit_l_max 57 _reflns.limit_l_min 0 _reflns.number_obs 7228 _reflns.observed_criterion '> 1 \s(I)' _reflns.details none ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. ; ; _reflns.limit_h_min 0 _reflns.limit_h_max 6 _reflns.limit_k_min 0 _reflns.limit_k_max 17 _reflns.limit_l_min 0 _reflns.limit_l_max 22 _reflns.number_all 1592 _reflns.number_obs 1408 _reflns.observed_criterion F_>_6.0_\s(F) _reflns.d_resolution_high 0.8733 _reflns.d_resolution_low 11.9202 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns.B_iso_Wilson_estimate _item_description.description ; The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot. ; _item.name '_reflns.B_iso_Wilson_estimate' _item.category_id reflns _item.mandatory_code no _item_type.code float _item_units.code angstroms_squared save_ save__reflns.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_reflns.entry_id' _item.mandatory_code yes save_ save__reflns.data_reduction_details _item_description.description ; A description of special aspects of the data-reduction procedures. ; _item.name '_reflns.data_reduction_details' _item.category_id reflns _item.mandatory_code no _item_type.code text _item_examples.case ; Merging and scaling based on only those reflections with I > sig(I). ; save_ save__reflns.data_reduction_method _item_description.description ; The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs. ; _item.name '_reflns.data_reduction_method' _item.category_id reflns _item.mandatory_code no _item_type.code text _item_examples.case ; Profile fitting by method of Kabsch (1987). Scaling used spherical harmonic coefficients. ; save_ save__reflns.d_resolution_high _item_description.description ; The smallest value for the interplanar spacings for the reflection data. This is called the highest resolution. ; _item.name '_reflns.d_resolution_high' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_d_resolution_high' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns.d_resolution_low _item_description.description ; The largest value for the interplanar spacings for the reflection data. This is called the lowest resolution. ; _item.name '_reflns.d_resolution_low' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_d_resolution_low' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns.details _item_description.description ; A description of reflection data not covered by other data names. This should include details of the Friedel pairs. ; _item.name '_reflns.details' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_special_details' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__reflns.limit_h_max _item_description.description ; Maximum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_max. ; _item.name '_reflns.limit_h_max' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_h_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_h_min _item_description.description ; Minimum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_min. ; _item.name '_reflns.limit_h_min' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_h_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_k_max _item_description.description ; Maximum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_max. ; _item.name '_reflns.limit_k_max' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_k_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_k_min _item_description.description ; Minimum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_min. ; _item.name '_reflns.limit_k_min' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_k_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_l_max _item_description.description ; Maximum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_max. ; _item.name '_reflns.limit_l_max' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_l_max' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.limit_l_min _item_description.description ; Minimum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_min. ; _item.name '_reflns.limit_l_min' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_limit_l_min' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns.number_all _item_description.description ; The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item _reflns.details describes the reflection data. ; _item.name '_reflns.number_all' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_number_total' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__reflns.number_obs _item_description.description ; The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see _reflns.observed_criterion). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. ; _item.name '_reflns.number_obs' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_number_observed' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__reflns.observed_criterion _item_description.description ; The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. ; _item.name '_reflns.observed_criterion' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_observed_criterion' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion_sigma_F' alternate '_reflns.observed_criterion_sigma_I' alternate '_reflns.observed_criterion_I_min' alternate '_reflns.observed_criterion_I_max' alternate '_reflns.observed_criterion_F_min' alternate '_reflns.observed_criterion_F_max' alternate _item_type.code text _item_examples.case '>2sigma(I)' save_ save__reflns.observed_criterion_F_max _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F. ; _item.name '_reflns.observed_criterion_F_max' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_I_max' convention _item_type.code float save_ save__reflns.observed_criterion_F_min _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F. ; _item.name '_reflns.observed_criterion_F_min' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_I_min' convention _item_type.code float save_ save__reflns.observed_criterion_I_max _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I. ; _item.name '_reflns.observed_criterion_I_max' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_F_max' convention _item_type.code float save_ save__reflns.observed_criterion_I_min _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I. ; _item.name '_reflns.observed_criterion_I_min' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_F_min' convention _item_type.code float save_ save__reflns.observed_criterion_sigma_F _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F). ; _item.name '_reflns.observed_criterion_sigma_F' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_sigma_I' convention _item_type.code float save_ save__reflns.observed_criterion_sigma_I _item_description.description ; The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I). ; _item.name '_reflns.observed_criterion_sigma_I' _item.category_id reflns _item.mandatory_code no loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate '_reflns.observed_criterion_sigma_F' convention _item_type.code float save_ save__reflns.percent_possible_obs _item_description.description ; The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. ; _item.name '_reflns.percent_possible_obs' _item.category_id reflns _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns.R_free_details _item_description.description ; A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor. ; _item.name '_reflns.R_free_details' _item.category_id reflns _item.mandatory_code no _item_type.code text _item_examples.case ; The data set was sorted with l varying most rapidly and h varying least rapidly. Every 10th reflection in this sorted list was excluded from refinement and included in the calculation of a 'free' R factor. ; save_ save__reflns.Rmerge_F_all _item_description.description ; Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns.Rmerge_F_all' _item.category_id reflns _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns.Rmerge_F_obs _item_description.description ; Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns.Rmerge_F_obs' _item.category_id reflns _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################## ## REFLNS_SCALE ## ################## save_reflns_scale _category.description ; Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through _refln.scale_group_code. ; _category.id reflns_scale _category.mandatory_code no _category_key.name '_reflns_scale.group_code' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. ; ; _reflns_scale.group_code SG1 _reflns_scale.meas_F 4.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns_scale.group_code _item_description.description ; The code identifying a scale _reflns_scale.meas_F, _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity. These are linked to the REFLN list by the _refln.scale_group_code. These codes need not correspond to those in the DIFFRN_SCALE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_reflns_scale.group_code' reflns_scale yes '_refln.scale_group_code' refln yes _item_aliases.alias_name '_reflns_scale_group_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_linked.child_name _item_linked.parent_name '_refln.scale_group_code' '_reflns_scale.group_code' _item_type.code line loop_ _item_examples.case '1' '2' 'c1' 'c2' save_ save__reflns_scale.meas_F _item_description.description ; A scale associated with _reflns_scale.group_code. ; _item.name '_reflns_scale.meas_F' _item.category_id reflns_scale _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_F' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_scale.meas_F_squared _item_description.description ; A scale associated with _reflns_scale.group_code. ; _item.name '_reflns_scale.meas_F_squared' _item.category_id reflns_scale _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_F_squared' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_scale.meas_intensity _item_description.description ; A scale associated with _reflns_scale.group_code. ; _item.name '_reflns_scale.meas_intensity' _item.category_id reflns_scale _item.mandatory_code no _item_aliases.alias_name '_reflns_scale_meas_intensity' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ################## ## REFLNS_SHELL ## ################## save_reflns_shell _category.description ; Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution. ; _category.id reflns_shell _category.mandatory_code no loop_ _category_key.name '_reflns_shell.d_res_high' '_reflns_shell.d_res_low' loop_ _category_group.id 'inclusive_group' 'refln_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_obs 31.38 3.82 69.8 9024 2540 96.8 1.98 3.82 3.03 26.1 7413 2364 95.1 3.85 3.03 2.65 10.5 5640 2123 86.2 6.37 2.65 2.41 6.4 4322 1882 76.8 8.01 2.41 2.23 4.3 3247 1714 70.4 9.86 2.23 2.10 3.1 1140 812 33.3 13.99 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns_shell.d_res_high _item_description.description ; The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. ; _item.name '_reflns_shell.d_res_high' _item.category_id reflns_shell _item.mandatory_code yes _item_aliases.alias_name '_reflns_shell_d_res_high' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns_shell.d_res_low _item_description.description ; The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. ; _item.name '_reflns_shell.d_res_low' _item.category_id reflns_shell _item.mandatory_code yes _item_aliases.alias_name '_reflns_shell_d_res_low' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__reflns_shell.meanI_over_sigI_all _item_description.description ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. ; _item.name '_reflns_shell.meanI_over_sigI_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_meanI_over_sigI_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__reflns_shell.meanI_over_sigI_obs _item_description.description ; The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns.observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell. ; _item.name '_reflns_shell.meanI_over_sigI_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_meanI_over_sigI_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float save_ save__reflns_shell.number_measured_all _item_description.description ; The total number of reflections measured for this shell. ; _item.name '_reflns_shell.number_measured_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_measured_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.number_measured_obs _item_description.description ; The number of reflections classified as 'observed' (see _reflns.observed_criterion) for this shell. ; _item.name '_reflns_shell.number_measured_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_measured_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.number_possible _item_description.description ; The number of unique reflections it is possible to measure in this shell. ; _item.name '_reflns_shell.number_possible' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_possible' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__reflns_shell.number_unique_all _item_description.description ; The total number of measured reflections which are symmetry- unique after merging for this shell. ; _item.name '_reflns_shell.number_unique_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_unique_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.number_unique_obs _item_description.description ; The total number of measured reflections classified as 'observed' (see _reflns.observed_criterion) which are symmetry-unique after merging for this shell. ; _item.name '_reflns_shell.number_unique_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_number_unique_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__reflns_shell.percent_possible_all _item_description.description ; The percentage of geometrically possible reflections represented by all reflections measured for this shell. ; _item.name '_reflns_shell.percent_possible_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_percent_possible_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.percent_possible_obs _item_description.description ; The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see _reflns.observed_criterion) for this shell. ; _item.name '_reflns_shell.percent_possible_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_percent_possible_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_F_all _item_description.description ; Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_F_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_F_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_F_obs _item_description.description ; Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum~i~(sum~j~|F~j~ - |) Rmerge(F) = -------------------------- sum~i~(sum~j~) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_F_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_F_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_I_all _item_description.description ; The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - |) Rmerge(I) = -------------------------- sum~i~(sum~j~) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_I_all' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_I_all' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__reflns_shell.Rmerge_I_obs _item_description.description ; The value of Rmerge(I) for reflections classified as 'observed' (see _reflns.observed_criterion) in a given shell. sum~i~(sum~j~|I~j~ - |) Rmerge(I) = -------------------------- sum~i~(sum~j~) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection ; _item.name '_reflns_shell.Rmerge_I_obs' _item.category_id reflns_shell _item.mandatory_code no _item_aliases.alias_name '_reflns_shell_Rmerge_I_obs' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ ############## ## SOFTWARE ## ############## save_software _category.description ; Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do. ; _category.id software _category.mandatory_code no loop_ _category_key.name '_software.name' '_software.version' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.location _software.classification _software.citation_id _software.language _software.compiler_name _software.compiler_version _software.hardware _software.os _software.os_version _software.dependencies _software.mods _software.description Prolsq unknown . program 'Wayne A. Hendrickson' ? 'ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/' refinement ref5 Fortran 'Convex Fortran' v8.0 'Convex C220' ConvexOS v10.1 'Requires that Protin be run first' optimized 'restrained least-squares refinement' ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__software.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_software.citation_id' _item.mandatory_code no save_ save__software.classification _item_description.description ; The classification of the program according to its major function. ; _item.name '_software.classification' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'data collection' 'data reduction' 'phasing' 'model building' 'refinement' 'validation' 'other' save_ save__software.compiler_name _item_description.description ; The compiler used to compile the software. ; _item.name '_software.compiler_name' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Convex Fortran' 'gcc' 'DEC C' save_ save__software.compiler_version _item_description.description ; The version of the compiler used to compile the software. ; _item.name '_software.compiler_version' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case '3.1' '2.1 alpha' save_ save__software.contact_author _item_description.description ; The recognized contact author of the software. This could be the original author, someone who has modified the code or someone who maintains the code. It should be the person most commonly associated with the code. ; _item.name '_software.contact_author' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'T. Alwyn Jones' 'Axel Brunger' save_ save__software.contact_author_email _item_description.description ; The e-mail address of the person specified in _software.contact_author. ; _item.name '_software.contact_author_email' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'bourne@sdsc.edu' save_ save__software.date _item_description.description ; The date the software was released. ; _item.name '_software.date' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 1991-10-01 1990-04-30 save_ save__software.description _item_description.description ; Description of the software. ; _item.name '_software.description' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'Uses method of restrained least squares' save_ save__software.dependencies _item_description.description ; Any prerequisite software required to run _software.name. ; _item.name '_software.dependencies' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'PDBlib class library' save_ save__software.hardware _item_description.description ; The hardware upon which the software was run. ; _item.name '_software.hardware' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Sun Sparc 10 model 41' 'Dec Alpha 3000 model 500S' 'Silicon Graphics Elan' 'Compaq PC 486/66' save_ save__software.language _item_description.description ; The major computing language in which the software is coded. ; _item.name '_software.language' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value Ada assembler Awk Basic 'C++' 'C/C++' C csh Fortran Fortran_77 'Fortran 77' 'Fortran 90' Java ksh Pascal Perl Python sh Tcl Other save_ save__software.location _item_description.description ; The URL for an Internet address at which details of the software can be found. ; _item.name '_software.location' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'http://rosebud.sdsc.edu/projects/pb/IUCr/software.html' 'ftp://ftp.sdsc.edu/pub/sdsc/biology/' save_ save__software.mods _item_description.description ; Any noteworthy modifications to the base software, if applicable. ; _item.name '_software.mods' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'Added support for space group F432' save_ save__software.name _item_description.description ; The name of the software. ; _item.name '_software.name' _item.category_id software _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'Merlot' 'O' 'Xengen' 'X-plor' save_ save__software.os _item_description.description ; The name of the operating system under which the software runs. ; _item.name '_software.os' _item.category_id software _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Ultrix' 'OpenVMS' 'DOS' 'Windows 95' 'Windows NT' 'Irix' 'HPUX' 'DEC Unix' save_ save__software.os_version _item_description.description ; The version of the operating system under which the software runs. ; _item.name '_software.os_version' _item.category_id software _item.mandatory_code no _item_type.code text loop_ _item_examples.case '3.1' '4.2.1' save_ save__software.type _item_description.description ; The classification of the software according to the most common types. ; _item.name '_software.type' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value _item_enumeration.detail program ; individual program with limited functionality ; library ; used by a program at load time ; package ; collections of programs with multiple functionality ; filter ; filters input and output streams ; jiffy ; short, simple program ; other ; all other kinds of software ; save_ save__software.version _item_description.description ; The version of the software. ; _item.name '_software.version' _item.category_id software _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'v1.0' 'beta' '3.1-2' 'unknown' save_ ############ ## STRUCT ## ############ save_struct _category.description ; Data items in the STRUCT category record details about the description of the crystallographic structure. ; _category.id struct _category.mandatory_code no _category_key.name '_struct.entry_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _struct.entry_id '5HVP' _struct.title ; HIV-1 protease complex with acetyl-pepstatin ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_struct.entry_id' _item.mandatory_code yes save_ save__struct.title _item_description.description ; A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. ; _item.name '_struct.title' _item.category_id struct _item.mandatory_code no _item_type.code text loop_ _item_examples.case '5'-D(*(I)CP*CP*GP*G)-3' 'T4 lysozyme mutant - S32A' 'hen egg white lysozyme at -30 degrees C' 'quail egg white lysozyme at 2 atmospheres' save_ ################# ## STRUCT_ASYM ## ################# save_struct_asym _category.description ; Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. ; _category.id struct_asym _category.mandatory_code no _category_key.name '_struct_asym.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_asym.id _struct_asym.entity_id _struct_asym.details A 1 'one monomer of the dimeric enzyme' B 1 'one monomer of the dimeric enzyme' C 2 'one partially occupied position for the inhibitor' D 2 'one partially occupied position for the inhibitor' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_asym.details _item_description.description ; A description of special aspects of this portion of the contents of the asymmetric unit. ; _item.name '_struct_asym.details' _item.category_id struct_asym _item.mandatory_code no _item_type.code text _item_examples.case ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. ; save_ save__struct_asym.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_struct_asym.entity_id' _item.mandatory_code yes save_ save__struct_asym.id _item_description.description ; The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_asym.id' struct_asym yes '_atom_site.label_asym_id' atom_site no '_geom_angle.atom_site_label_asym_id_1' geom_angle no '_geom_angle.atom_site_label_asym_id_2' geom_angle no '_geom_angle.atom_site_label_asym_id_3' geom_angle no '_geom_bond.atom_site_label_asym_id_1' geom_bond no '_geom_bond.atom_site_label_asym_id_2' geom_bond no '_geom_contact.atom_site_label_asym_id_1' geom_contact no '_geom_contact.atom_site_label_asym_id_2' geom_contact no '_geom_hbond.atom_site_label_asym_id_A' geom_hbond no '_geom_hbond.atom_site_label_asym_id_D' geom_hbond no '_geom_hbond.atom_site_label_asym_id_H' geom_hbond no '_geom_torsion.atom_site_label_asym_id_1' geom_torsion no '_geom_torsion.atom_site_label_asym_id_2' geom_torsion no '_geom_torsion.atom_site_label_asym_id_3' geom_torsion no '_geom_torsion.atom_site_label_asym_id_4' geom_torsion no '_struct_biol_gen.asym_id' struct_biol_gen yes '_struct_conf.beg_label_asym_id' struct_conf yes '_struct_conf.end_label_asym_id' struct_conf yes '_struct_conn.ptnr1_label_asym_id' struct_conn yes '_struct_conn.ptnr2_label_asym_id' struct_conn yes '_struct_mon_nucl.label_asym_id' struct_mon_nucl yes '_struct_mon_prot.label_asym_id' struct_mon_prot yes '_struct_mon_prot_cis.label_asym_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_asym_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_asym_id' struct_ncs_dom_lim yes '_struct_sheet_range.beg_label_asym_id' struct_sheet_range yes '_struct_sheet_range.end_label_asym_id' struct_sheet_range yes '_struct_site_gen.label_asym_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_asym_id' '_struct_asym.id' '_struct_biol_gen.asym_id' '_struct_asym.id' '_geom_angle.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_angle.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_angle.atom_site_label_asym_id_3' '_atom_site.label_asym_id' '_geom_bond.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_bond.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_contact.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_contact.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_hbond.atom_site_label_asym_id_A' '_atom_site.label_asym_id' '_geom_hbond.atom_site_label_asym_id_D' '_atom_site.label_asym_id' '_geom_hbond.atom_site_label_asym_id_H' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_1' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_2' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_3' '_atom_site.label_asym_id' '_geom_torsion.atom_site_label_asym_id_4' '_atom_site.label_asym_id' '_struct_conf.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_conf.end_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr1_label_asym_id' '_atom_site.label_asym_id' '_struct_conn.ptnr2_label_asym_id' '_atom_site.label_asym_id' '_struct_mon_nucl.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot.label_asym_id' '_atom_site.label_asym_id' '_struct_mon_prot_cis.label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_lim.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_ncs_dom_lim.end_label_asym_id' '_atom_site.label_asym_id' '_struct_sheet_range.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_sheet_range.end_label_asym_id' '_atom_site.label_asym_id' '_struct_site_gen.label_asym_id' '_atom_site.label_asym_id' _item_type.code code loop_ _item_examples.case '1' 'A' '2B3' save_ ################# ## STRUCT_BIOL ## ################# save_struct_biol _category.description ; Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit. ; _category.id struct_biol _category.mandatory_code no _category_key.name '_struct_biol.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_biol.id _struct_biol.details 1 ; significant deviations from twofold symmetry exist in this dimeric enzyme ; 2 ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (2) is roughly twofold symmetric to biological unit (3). Disorder in the protein chain indicated with alternative ID 1 should be used with this biological unit. ; 3 ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol.details _item_description.description ; A description of special aspects of the biological unit. ; _item.name '_struct_biol.details' _item.category_id struct_biol _item.mandatory_code no _item_type.code text _item_examples.case ; The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. ; save_ save__struct_biol.id _item_description.description ; The value of _struct_biol.id must uniquely identify a record in the STRUCT_BIOL list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_biol.id' struct_biol yes '_struct_biol_gen.biol_id' struct_biol_gen yes '_struct_biol_keywords.biol_id' struct_biol_keywords yes '_struct_biol_view.biol_id' struct_biol_view yes '_struct_ref.biol_id' struct_ref no loop_ _item_linked.child_name _item_linked.parent_name '_struct_biol_gen.biol_id' '_struct_biol.id' '_struct_biol_keywords.biol_id' '_struct_biol.id' '_struct_biol_view.biol_id' '_struct_biol.id' '_struct_ref.biol_id' '_struct_biol.id' _item_type.code line save_ ##################### ## STRUCT_BIOL_GEN ## ##################### save_struct_biol_gen _category.description ; Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements. ; _category.id struct_biol_gen _category.mandatory_code no loop_ _category_key.name '_struct_biol_gen.biol_id' '_struct_biol_gen.asym_id' '_struct_biol_gen.symmetry' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry 1 A 1_555 1 B 1_555 2 A 1_555 2 B 1_555 2 C 1_555 3 A 1_555 3 B 1_555 3 D 1_555 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol_gen.asym_id _item_description.description ; This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_struct_biol_gen.asym_id' _item.mandatory_code yes save_ save__struct_biol_gen.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_biol_gen.biol_id' _item.mandatory_code yes save_ save__struct_biol_gen.details _item_description.description ; A description of special aspects of the symmetry generation of this portion of the biological structure. ; _item.name '_struct_biol_gen.details' _item.category_id struct_biol_gen _item.mandatory_code no _item_type.code text _item_examples.case ; The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. ; save_ save__struct_biol_gen.symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_biol_gen.asym_id to generate a portion of the biological structure. ; _item.name '_struct_biol_gen.symmetry' _item.category_id struct_biol_gen _item.mandatory_code yes # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ########################## ## STRUCT_BIOL_KEYWORDS ## ########################## save_struct_biol_keywords _category.description ; Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit. ; _category.id struct_biol_keywords _category.mandatory_code no loop_ _category_key.name '_struct_biol_keywords.biol_id' '_struct_biol_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_biol_keywords.biol_id _struct_biol_keywords.text 1 'aspartyl-protease' 1 'aspartic-protease' 1 'acid-protease' 1 'aspartyl-proteinase' 1 'aspartic-proteinase' 1 'acid-proteinase' 1 'enzyme' 1 'protease' 1 'proteinase' 1 'dimer' 2 'drug-enzyme complex' 2 'inhibitor-enzyme complex' 2 'drug-protease complex' 2 'inhibitor-protease complex' 3 'drug-enzyme complex' 3 'inhibitor-enzyme complex' 3 'drug-protease complex' 3 'inhibitor-protease complex' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol_keywords.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_biol_keywords.biol_id' _item.mandatory_code yes save_ save__struct_biol_keywords.text _item_description.description ; Keywords describing this biological entity. ; _item.name '_struct_biol_keywords.text' _item.category_id struct_biol_keywords _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'antibody' 'antigen' 'enzyme' 'cytokine' 'tRNA' save_ ###################### ## STRUCT_BIOL_VIEW ## ###################### save_struct_biol_view _category.description ; Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure. ; _category.id struct_biol_view _category.mandatory_code no loop_ _category_key.name '_struct_biol_view.biol_id' '_struct_biol_view.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry, (1989), 28, 310-320]. ; ; _struct_biol_view.biol_id c1 _struct_biol_view.id 1 _struct_biol_view.rot_matrix[1][1] 0.132 _struct_biol_view.rot_matrix[1][2] 0.922 _struct_biol_view.rot_matrix[1][3] -0.363 _struct_biol_view.rot_matrix[2][1] 0.131 _struct_biol_view.rot_matrix[2][2] -0.380 _struct_biol_view.rot_matrix[2][3] -0.916 _struct_biol_view.rot_matrix[3][1] -0.982 _struct_biol_view.rot_matrix[3][2] 0.073 _struct_biol_view.rot_matrix[3][3] -0.172 _struct_biol_view.details ; This view highlights the ATAT-Netropsin interaction in the DNA-drug complex. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_biol_view.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_biol_view.biol_id' _item.mandatory_code yes save_ save__struct_biol_view.details _item_description.description ; A description of special aspects of this view of the biological structure. This data item can be used as a figure legend. ; _item.name '_struct_biol_view.details' _item.category_id struct_biol_view _item.mandatory_code no _item_type.code text _item_examples.case ; The enzyme has been oriented with the molecular twofold axis aligned with the horizontal axis of the figure. ; save_ save__struct_biol_view.id _item_description.description ; The value of _struct_biol_view.id must uniquely identify a record in the STRUCT_BIOL_VIEW list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_biol_view.id' _item.category_id struct_biol_view _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Figure 1' 'unliganded enzyme' 'view down enzyme active site' save_ save__struct_biol_view.rot_matrix[1][1] _item_description.description ; The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[1][1]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[1][2] _item_description.description ; The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[1][2]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[1][3] _item_description.description ; The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[1][3]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[2][1] _item_description.description ; The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[2][1]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[2][2] _item_description.description ; The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[2][2]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[2][3] _item_description.description ; The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[2][3]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[3][1] _item_description.description ; The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[3][1]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[3][2] _item_description.description ; The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[3][2]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_biol_view.rot_matrix[3][3] _item_description.description ; The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_biol_view.rot_matrix[3][3]' _item.category_id struct_biol_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ ################# ## STRUCT_CONF ## ################# save_struct_conf _category.description ; Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations. ; _category.id struct_conf _category.mandatory_code no _category_key.name '_struct_conf.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conf.id _struct_conf.conf_type_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.details HELX1 HELX_RH_AL_P ARG A 87 GLN A 92 . HELX2 HELX_RH_AL_P ARG B 287 GLN B 292 . STRN1 STRN_P PRO A 1 LEU A 5 . STRN2 STRN_P CYS B 295 PHE B 299 . STRN3 STRN_P CYS A 95 PHE A 299 . STRN4 STRN_P PRO B 201 LEU B 205 . # - - - - data truncated for brevity - - - - TURN1 TURN_TY1P_P ILE A 15 GLN A 18 . TURN2 TURN_TY2_P GLY A 49 GLY A 52 . TURN3 TURN_TY1P_P ILE A 55 HIS A 69 . TURN4 TURN_TY1_P THR A 91 GLY A 94 . # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conf.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_conf.beg_label_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_comp_id' _item.mandatory_code yes save_ save__struct_conf.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_conf.beg_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_conf.beg_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_conf.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_conf.conf_type_id _item_description.description ; This data item is a pointer to _struct_conf_type.id in the STRUCT_CONF_TYPE category. ; _item.name '_struct_conf.conf_type_id' _item.mandatory_code yes save_ save__struct_conf.details _item_description.description ; A description of special aspects of the conformation assignment. ; _item.name '_struct_conf.details' _item.category_id struct_conf _item.mandatory_code no _item_type.code text save_ save__struct_conf.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_asym_id' _item.mandatory_code yes save_ save__struct_conf.end_label_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_comp_id' _item.mandatory_code yes save_ save__struct_conf.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_seq_id' _item.mandatory_code yes save_ save__struct_conf.end_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_asym_id' _item.mandatory_code no save_ save__struct_conf.end_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_comp_id' _item.mandatory_code no save_ save__struct_conf.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_seq_id' _item.mandatory_code no save_ save__struct_conf.id _item_description.description ; The value of _struct_conf.id must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conf.id' _item.category_id struct_conf _item.mandatory_code yes _item_type.code code save_ ###################### ## STRUCT_CONF_TYPE ## ###################### save_struct_conf_type _category.description ; Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer. ; _category.id struct_conf_type _category.mandatory_code no _category_key.name '_struct_conf_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conf_type.id _struct_conf_type.criteria _struct_conf_type.reference HELX_RH_AL_P 'author judgement' . STRN_P 'author judgement' . TURN_TY1_P 'author judgement' . TURN_TY1P_P 'author judgement' . TURN_TY2_P 'author judgement' . TURN_TY2P_P 'author judgement' . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conf_type.criteria _item_description.description ; The criteria used to assign this conformation type. ; _item.name '_struct_conf_type.criteria' _item.category_id struct_conf_type _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'author judgement' 'phi=54-74, psi=30-50' save_ save__struct_conf_type.id _item_description.description ; The descriptor that categorizes the type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsion angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conf_type.id' struct_conf_type yes '_struct_conf.conf_type_id' struct_conf yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.conf_type_id' '_struct_conf_type.id' _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail HELX_P ; helix with handedness and type not specified (protein) ; HELX_OT_P ; helix with handedness and type that do not conform to an accepted category (protein) ; # HELX_RH_P ; right-handed helix with type not specified (protein) ; HELX_RH_OT_P ; right-handed helix with type that does not conform to an accepted category (protein) ; HELX_RH_AL_P 'right-handed alpha helix (protein)' HELX_RH_GA_P 'right-handed gamma helix (protein)' HELX_RH_OM_P 'right-handed omega helix (protein)' HELX_RH_PI_P 'right-handed pi helix (protein)' HELX_RH_27_P 'right-handed 2-7 helix (protein)' HELX_RH_3T_P 'right-handed 3-10 helix (protein)' HELX_RH_PP_P 'right-handed polyproline helix (protein)' # HELX_LH_P ; left-handed helix with type not specified (protein) ; HELX_LH_OT_P ; left-handed helix with type that does not conform to an accepted category (protein) ; HELX_LH_AL_P 'left-handed alpha helix (protein)' HELX_LH_GA_P 'left-handed gamma helix (protein)' HELX_LH_OM_P 'left-handed omega helix (protein)' HELX_LH_PI_P 'left-handed pi helix (protein)' HELX_LH_27_P 'left-handed 2-7 helix (protein)' HELX_LH_3T_P 'left-handed 3-10 helix (protein)' HELX_LH_PP_P 'left-handed polyproline helix (protein)' # HELX_N ; helix with handedness and type not specified (nucleic acid) ; HELX_OT_N ; helix with handedness and type that do not conform to an accepted category (nucleic acid) ; # HELX_RH_N ; right-handed helix with type not specified (nucleic acid) ; HELX_RH_OT_N ; right-handed helix with type that does not conform to an accepted category (nucleic acid) ; HELX_RH_A_N 'right-handed A helix (nucleic acid)' HELX_RH_B_N 'right-handed B helix (nucleic acid)' HELX_RH_Z_N 'right-handed Z helix (nucleic acid)' # HELX_LH_N ; left-handed helix with type not specified (nucleic acid) ; HELX_LH_OT_N ; left-handed helix with type that does not conform to an accepted category (nucleic acid) ; HELX_LH_A_N 'left-handed A helix (nucleic acid)' HELX_LH_B_N 'left-handed B helix (nucleic acid)' HELX_LH_Z_N 'left-handed Z helix (nucleic acid)' # TURN_P 'turn with type not specified (protein)' TURN_OT_P ; turn with type that does not conform to an accepted category (protein) ; TURN_TY1_P 'type I turn (protein)' TURN_TY1P_P 'type I prime turn (protein)' TURN_TY2_P 'type II turn (protein)' TURN_TY2P_P 'type II prime turn (protein)' TURN_TY3_P 'type III turn (protein)' TURN_TY3P_P 'type III prime turn (protein)' # STRN 'beta strand (protein)' save_ save__struct_conf_type.reference _item_description.description ; A literature reference that defines the criteria used to assign this conformation type and subtype. ; _item.name '_struct_conf_type.reference' _item.category_id struct_conf_type _item.mandatory_code no _item_type.code text save_ ################# ## STRUCT_CONN ## ################# save_struct_conn _category.description ; Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections. ; _category.id struct_conn _category.mandatory_code no _category_key.name '_struct_conn.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_role _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_role _struct_conn.ptnr2_symmetry _struct_conn.details C1 saltbr ARG A 87 NZ1 positive 1_555 GLU A 92 OE1 negative 1_555 . C2 hydrog ARG B 287 N donor 1_555 GLY B 292 O acceptor 1_555 . # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conn.conn_type_id _item_description.description ; This data item is a pointer to _struct_conn_type.id in the STRUCT_CONN_TYPE category. ; _item.name '_struct_conn.conn_type_id' _item.mandatory_code yes save_ save__struct_conn.details _item_description.description ; A description of special aspects of the connection. ; _item.name '_struct_conn.details' _item.category_id struct_conn _item.mandatory_code no _item_type.code text _item_examples.case 'disulfide bridge C-S-S-C is highly distorted' save_ save__struct_conn.id _item_description.description ; The value of _struct_conn.id must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conn.id' _item.category_id struct_conn _item.mandatory_code yes _item_type.code code save_ save__struct_conn.ptnr1_label_alt_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_conn.ptnr1_label_alt_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_label_asym_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_label_asym_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_label_atom_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_struct_conn.ptnr1_label_atom_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_label_comp_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_label_comp_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_label_seq_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_label_seq_id' _item.mandatory_code yes save_ save__struct_conn.ptnr1_auth_asym_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_asym_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_auth_atom_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_atom_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_auth_comp_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_comp_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_auth_seq_id _item_description.description ; A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr1_auth_seq_id' _item.mandatory_code no save_ save__struct_conn.ptnr1_role _item_description.description ; The chemical or structural role of the first partner in the structure connection. ; _item.name '_struct_conn.ptnr1_role' _item.category_id struct_conn _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'donor' 'acceptor' 'negative' 'positive' 'metal' 'metal coordination' save_ save__struct_conn.ptnr1_symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr1_label* to generate the first partner in the structure connection. ; _item.name '_struct_conn.ptnr1_symmetry' _item.category_id struct_conn _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ save__struct_conn.ptnr2_label_alt_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_conn.ptnr2_label_alt_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_label_asym_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_label_asym_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_label_atom_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_struct_conn.ptnr2_label_atom_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_label_comp_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_label_comp_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_label_seq_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_label_seq_id' _item.mandatory_code yes save_ save__struct_conn.ptnr2_auth_asym_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_asym_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_auth_atom_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_atom_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_auth_comp_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_comp_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_auth_seq_id _item_description.description ; A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conn.ptnr2_auth_seq_id' _item.mandatory_code no save_ save__struct_conn.ptnr2_role _item_description.description ; The chemical or structural role of the second partner in the structure connection. ; _item.name '_struct_conn.ptnr2_role' _item.category_id struct_conn _item.mandatory_code no _item_type.code uline loop_ _item_examples.case 'donor' 'acceptor' 'negative' 'positive' 'metal' 'metal coordination' save_ save__struct_conn.ptnr2_symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr2_label* to generate the second partner in the structure connection. ; _item.name '_struct_conn.ptnr2_symmetry' _item.category_id struct_conn _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ###################### ## STRUCT_CONN_TYPE ## ###################### save_struct_conn_type _category.description ; Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure. ; _category.id struct_conn_type _category.mandatory_code no _category_key.name '_struct_conn_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference saltbr 'negative to positive distance > 2.5 \%A, < 3.2 \%A' . hydrog 'NO distance > 2.5\%A, < 3.5\%A, NOC angle < 120 degrees' . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conn_type.criteria _item_description.description ; The criteria used to define the interaction. ; _item.name '_struct_conn_type.criteria' _item.category_id struct_conn_type _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'O to N distance > 2.5 \%A, < 3.2 \%A' 'authors judgement' save_ save__struct_conn_type.id _item_description.description ; The chemical or structural type of the interaction. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conn_type.id' struct_conn_type yes '_struct_conn.conn_type_id' struct_conn yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conn.conn_type_id' '_struct_conn_type.id' _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail covale 'covalent bond' disulf 'disulfide bridge' hydrog 'hydrogen bond' metalc 'metal coordination' mismat 'mismatched base pairs' saltbr 'ionic interaction' modres 'covalent residue modification' covale_base 'covalent modification of a nucleotide base' covale_sugar 'covalent modification of a nucleotide sugar' covale_phosphate 'covalent modification of a nucleotide phosphate' save_ save__struct_conn_type.reference _item_description.description ; A reference that specifies the criteria used to define the interaction. ; _item.name '_struct_conn_type.reference' _item.category_id struct_conn_type _item.mandatory_code no _item_type.code text save_ ##################### ## STRUCT_KEYWORDS ## ##################### save_struct_keywords _category.description ; Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry. ; _category.id struct_keywords _category.mandatory_code no loop_ _category_key.name '_struct_keywords.entry_id' # '_struct_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_keywords.entry_id _struct_keywords.text '5HVP' 'enzyme-inhibitor complex' '5HVP' 'aspartyl protease' '5HVP' 'structure-based drug design' '5HVP' 'static disorder' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_keywords.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_struct_keywords.entry_id' _item.mandatory_code yes save_ save__struct_keywords.text _item_description.description ; Keywords describing this structure. ; _item.name '_struct_keywords.text' _item.category_id struct_keywords _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'serine protease' 'inhibited complex' 'high-resolution refinement' save_ ######################## ## STRUCT_MON_DETAILS ## ######################## save_struct_mon_details _category.description ; Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on. ; _category.id struct_mon_details _category.mandatory_code no _category_key.name '_struct_mon_details.entry_id' loop_ _category_group.id 'inclusive_group' 'struct_group' save_ save__struct_mon_details.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_struct_mon_details.entry_id' _item.mandatory_code yes save_ save__struct_mon_details.prot_cis _item_description.description ; An ideal cis peptide bond would have an omega torsion angle of zero. This data item gives the value in degrees by which the observed torsion angle can differ from 0.0 and still be considered cis. ; _item.name '_struct_mon_details.prot_cis' _item.category_id struct_mon_details _item.mandatory_code no _item_type.code float _item_units.code degrees _item_examples.case 30.0 save_ save__struct_mon_details.RSCC _item_description.description ; This data item describes the specifics of the calculations that generated the values given in _struct_mon_prot.RSCC_all, _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. ; _item.name '_struct_mon_details.RSCC' _item.category_id struct_mon_details _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. ; ; The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. ; save_ save__struct_mon_details.RSR _item_description.description ; This data item describes the specifics of the calculations that generated the values given in _struct_mon_prot.RSR_all, _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. ; _item.name '_struct_mon_details.RSR' _item.category_id struct_mon_details _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. ; ; The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. ; save_ ##################### ## STRUCT_MON_NUCL ## ##################### save_struct_mon_nucl _category.description ; Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. ; _category.id struct_mon_nucl _category.mandatory_code no loop_ _category_key.name '_struct_mon_nucl.label_alt_id' '_struct_mon_nucl.label_asym_id' '_struct_mon_nucl.label_comp_id' '_struct_mon_nucl.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure BDL028. ; ; loop_ _struct_mon_nucl.label_comp_id _struct_mon_nucl.label_seq_id _struct_mon_nucl.label_asym_id _struct_mon_nucl.label_alt_id _struct_mon_nucl.alpha _struct_mon_nucl.beta _struct_mon_nucl.gamma _struct_mon_nucl.delta _struct_mon_nucl.epsilon _struct_mon_nucl.zeta C 1 A . . . 29.9 131.9 222.1 174.2 G 2 A . 334.0 130.6 33.1 125.6 167.6 270.9 T 3 A . 258.2 178.7 101.0 114.6 216.6 259.3 # ---- abbreviated list ----- ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_mon_nucl.alpha _item_description.description ; The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5'). ; _item.name '_struct_mon_nucl.alpha' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.auth_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.auth_asym_id' _item.mandatory_code no save_ save__struct_mon_nucl.auth_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.auth_comp_id' _item.mandatory_code no save_ save__struct_mon_nucl.auth_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.auth_seq_id' _item.mandatory_code no save_ save__struct_mon_nucl.beta _item_description.description ; The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4'). ; _item.name '_struct_mon_nucl.beta' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.chi1 _item_description.description ; The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2). ; _item.name '_struct_mon_nucl.chi1' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.chi2 _item_description.description ; The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4). ; _item.name '_struct_mon_nucl.chi2' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.delta _item_description.description ; The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3'). ; _item.name '_struct_mon_nucl.delta' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.details _item_description.description ; A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. ; _item.name '_struct_mon_nucl.details' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_examples.case ; Part of the phosphodiester backbone not in density. ; save_ save__struct_mon_nucl.epsilon _item_description.description ; The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P). ; _item.name '_struct_mon_nucl.epsilon' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.gamma _item_description.description ; The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3'). ; _item.name '_struct_mon_nucl.gamma' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.label_alt_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_mon_nucl.label_alt_id' _item.mandatory_code yes save_ save__struct_mon_nucl.label_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.label_asym_id' _item.mandatory_code yes save_ save__struct_mon_nucl.label_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.label_comp_id' _item.mandatory_code yes save_ save__struct_mon_nucl.label_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_nucl.label_seq_id' _item.mandatory_code yes save_ save__struct_mon_nucl.mean_B_all _item_description.description ; The mean value of the isotropic displacement parameter for all atoms in the monomer. ; _item.name '_struct_mon_nucl.mean_B_all' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.mean_B_base _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_base' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.mean_B_phos _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_phos' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.mean_B_sugar _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer. ; _item.name '_struct_mon_nucl.mean_B_sugar' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.nu0 _item_description.description ; The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2'). ; _item.name '_struct_mon_nucl.nu0' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu1 _item_description.description ; The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3'). ; _item.name '_struct_mon_nucl.nu1' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu2 _item_description.description ; The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4'). ; _item.name '_struct_mon_nucl.nu2' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu3 _item_description.description ; The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4'). ; _item.name '_struct_mon_nucl.nu3' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.nu4 _item_description.description ; The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1'). ; _item.name '_struct_mon_nucl.nu4' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.P _item_description.description ; P is the phase angle of pseudorotation for five-membered rings. For ribose and deoxyribose sugars in nucleic acids (tau4 +tau1)-(tau3+tau0) P = ATAN (-------------------------) 2tau2 (sin 36+sin 72) If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam, 1972). Ref: Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212. ; _item.name '_struct_mon_nucl.P' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.RSCC_all _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_all' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSCC_base _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_base' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSCC_phos _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_phos' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSCC_sugar _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_nucl.RSCC_sugar' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_all _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_all' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_base _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_base' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_phos _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_phos' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.RSR_sugar _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_nucl.RSR_sugar' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float save_ save__struct_mon_nucl.tau0 _item_description.description ; The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2'). ; _item.name '_struct_mon_nucl.tau0' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau1 _item_description.description ; The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3'). ; _item.name '_struct_mon_nucl.tau1' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau2 _item_description.description ; The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4'). ; _item.name '_struct_mon_nucl.tau2' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau3 _item_description.description ; The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4'). ; _item.name '_struct_mon_nucl.tau3' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.tau4 _item_description.description ; The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1'). ; _item.name '_struct_mon_nucl.tau4' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.taum _item_description.description ; The maximum amplitude of puckering. This is derived from the pseudorotation value P and the torsion angles in the ribose ring. Tau2= Taum cosP Tau3= Taum cos(P+144) Tau4= Taum cos(P+288) Tau0= Taum cos(P+ 72) Tau1= Taum cos(P+216) ; _item.name '_struct_mon_nucl.taum' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_nucl.zeta _item_description.description ; The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5'). ; _item.name '_struct_mon_nucl.zeta' _item.category_id struct_mon_nucl _item.mandatory_code no _item_type.code float _item_units.code degrees save_ ##################### ## STRUCT_MON_PROT ## ##################### save_struct_mon_prot _category.description ; Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. ; _category.id struct_mon_prot _category.mandatory_code no loop_ _category_key.name '_struct_mon_prot.label_alt_id' '_struct_mon_prot.label_asym_id' '_struct_mon_prot.label_comp_id' '_struct_mon_prot.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for protein NS1. This example provides details for residue ARG 35. ; ; _struct_mon_prot.label_comp_id ARG _struct_mon_prot.label_seq_id 35 _struct_mon_prot.label_asym_id A _struct_mon_prot.label_alt_id . _struct_mon_prot.chi1 -67.9 _struct_mon_prot.chi2 -174.7 _struct_mon_prot.chi3 -67.7 _struct_mon_prot.chi4 -86.3 _struct_mon_prot.chi5 4.2 _struct_mon_prot.RSCC_all 0.90 _struct_mon_prot.RSR_all 0.18 _struct_mon_prot.mean_B_all 30.0 _struct_mon_prot.mean_B_main 25.0 _struct_mon_prot.mean_B_side 35.1 _struct_mon_prot.omega 180.1 _struct_mon_prot.phi -60.3 _struct_mon_prot.psi -46.0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_mon_prot.chi1 _item_description.description ; The value in degrees of the side-chain torsion angle chi1, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi1' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi2 _item_description.description ; The value in degrees of the side-chain torsion angle chi2, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi2' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi3 _item_description.description ; The value in degrees of the side-chain torsion angle chi3, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi3' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi4 _item_description.description ; The value in degrees of the side-chain torsion angle chi4, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi4' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.chi5 _item_description.description ; The value in degrees of the side-chain torsion angle chi5, for those residues containing such an angle. ; _item.name '_struct_mon_prot.chi5' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.details _item_description.description ; A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. ; _item.name '_struct_mon_prot.details' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float loop_ _item_examples.case 'very poor density' ; The side chain of this density may occupy alternative conformations, but alternative conformations were not fit in this model. ; ; This residue has a close contact with the bound inhibitor, which may account for the nonstandard conformation of the side chain. ; save_ save__struct_mon_prot.label_alt_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_mon_prot.label_alt_id' _item.mandatory_code yes save_ save__struct_mon_prot.label_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.label_asym_id' _item.mandatory_code yes save_ save__struct_mon_prot.label_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.label_comp_id' _item.mandatory_code yes save_ save__struct_mon_prot.label_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.label_seq_id' _item.mandatory_code yes save_ save__struct_mon_prot.auth_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.auth_asym_id' _item.mandatory_code no save_ save__struct_mon_prot.auth_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.auth_comp_id' _item.mandatory_code no save_ save__struct_mon_prot.auth_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot.auth_seq_id' _item.mandatory_code no save_ save__struct_mon_prot.RSCC_all _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_prot.RSCC_all' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSCC_main _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_prot.RSCC_main' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSCC_side _item_description.description ; The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - | * sum|p~calc~ - | RSCC = ------------------------------------------------- [ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. ; _item.name '_struct_mon_prot.RSCC_side' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSR_all _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_prot.RSR_all' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSR_main _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_prot.RSR_main' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.RSR_side _item_description.description ; The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. ; _item.name '_struct_mon_prot.RSR_side' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.mean_B_all _item_description.description ; The mean value of the isotropic displacement parameter for all atoms in the monomer. ; _item.name '_struct_mon_prot.mean_B_all' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.mean_B_main _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the main chain of the monomer. ; _item.name '_struct_mon_prot.mean_B_main' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.mean_B_side _item_description.description ; The mean value of the isotropic displacement parameter for atoms in the side chain of the monomer. ; _item.name '_struct_mon_prot.mean_B_side' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float save_ save__struct_mon_prot.omega _item_description.description ; The value in degrees of the main-chain torsion angle omega. ; _item.name '_struct_mon_prot.omega' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.phi _item_description.description ; The value in degrees of the main-chain torsion angle phi. ; _item.name '_struct_mon_prot.phi' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ save__struct_mon_prot.psi _item_description.description ; The value in degrees of the main-chain torsion angle psi. ; _item.name '_struct_mon_prot.psi' _item.category_id struct_mon_prot _item.mandatory_code no _item_type.code float _item_units.code degrees save_ ######################### ## STRUCT_MON_PROT_CIS ## ######################### save_struct_mon_prot_cis _category.description ; Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in _struct_mon_details.prot_cis. ; _category.id struct_mon_prot_cis _category.mandatory_code no loop_ _category_key.name '_struct_mon_prot_cis.label_alt_id' '_struct_mon_prot_cis.label_asym_id' '_struct_mon_prot_cis.label_comp_id' '_struct_mon_prot_cis.label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield, Profy & Wilson [Science (1994), 264, 82-85]. ; ; loop_ _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id PRO 8 L . PRO 77 L . PRO 95 L . PRO 141 L . # ----- abbreviated ----- ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_mon_prot_cis.label_alt_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_mon_prot_cis.label_alt_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.label_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.label_asym_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.label_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.label_comp_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.label_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.label_seq_id' _item.mandatory_code yes save_ save__struct_mon_prot_cis.auth_asym_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.auth_asym_id' _item.mandatory_code no save_ save__struct_mon_prot_cis.auth_comp_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.auth_comp_id' _item.mandatory_code no save_ save__struct_mon_prot_cis.auth_seq_id _item_description.description ; A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_mon_prot_cis.auth_seq_id' _item.mandatory_code no save_ #################### ## STRUCT_NCS_DOM ## #################### save_struct_ncs_dom _category.description ; Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain. ; _category.id struct_ncs_dom _category.mandatory_code no _category_key.name '_struct_ncs_dom.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; loop_ _struct_ncs_dom.id _struct_ncs_dom.details d1 'Chains A, B, and C' d2 'Chains D, E, and F' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_dom.details _item_description.description ; A description of special aspects of the structural elements that comprise a domain in an ensemble of domains related by noncrystallographic symmetry. ; _item.name '_struct_ncs_dom.details' _item.category_id struct_ncs_dom _item.mandatory_code no _item_type.code text _item_examples.case ; The loop between residues 18 and 23 in this domain interacts with a symmetry-related molecule, and thus deviates significantly from the noncrystallographic threefold. ; save_ save__struct_ncs_dom.id _item_description.description ; The value of _struct_ncs_dom.id must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_dom.id' struct_ncs_dom yes '_struct_ncs_dom_lim.dom_id' struct_ncs_dom_lim yes '_struct_ncs_ens_gen.dom_id_1' struct_ncs_ens_gen yes '_struct_ncs_ens_gen.dom_id_2' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_dom_lim.dom_id' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_dom.id' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_dom.id' _item_type.code code save_ ######################## ## STRUCT_NCS_DOM_LIM ## ######################## save_struct_ncs_dom_lim _category.description ; Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry. ; _category.id struct_ncs_dom_lim _category.mandatory_code no loop_ _category_key.name '_struct_ncs_dom_lim.dom_id' '_struct_ncs_dom_lim.beg_label_alt_id' '_struct_ncs_dom_lim.beg_label_asym_id' '_struct_ncs_dom_lim.beg_label_comp_id' '_struct_ncs_dom_lim.beg_label_seq_id' '_struct_ncs_dom_lim.end_label_alt_id' '_struct_ncs_dom_lim.end_label_asym_id' '_struct_ncs_dom_lim.end_label_comp_id' '_struct_ncs_dom_lim.end_label_seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; loop_ _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id d1 . A PRO 1 . A GLY 29 d1 . B PRO 31 . B GLY 59 d1 . C PRO 61 . B GLY 89 d2 . D PRO 91 . D GLY 119 d2 . E PRO 121 . E GLY 149 d2 . F PRO 151 . F GLY 179 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_dom_lim.beg_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_ncs_dom_lim.beg_label_alt_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_label_comp_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.beg_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.beg_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.beg_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.dom_id _item_description.description ; This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_struct_ncs_dom_lim.dom_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_alt_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_ncs_dom_lim.end_label_alt_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_label_asym_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_label_comp_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_label_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_label_seq_id' _item.mandatory_code yes save_ save__struct_ncs_dom_lim.end_auth_asym_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_auth_asym_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.end_auth_comp_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_auth_comp_id' _item.mandatory_code no save_ save__struct_ncs_dom_lim.end_auth_seq_id _item_description.description ; A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_ncs_dom_lim.end_auth_seq_id' _item.mandatory_code no save_ #################### ## STRUCT_NCS_ENS ## #################### save_struct_ncs_ens _category.description ; Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description. ; _category.id struct_ncs_ens _category.mandatory_code no _category_key.name '_struct_ncs_ens.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; _struct_ncs_ens.id en1 _struct_ncs_ens.details ; The ensemble represents the pseudo-twofold symmetry between domains d1 and d2. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_ens.details _item_description.description ; A description of special aspects of the ensemble. ; _item.name '_struct_ncs_ens.details' _item.category_id struct_ncs_ens _item.mandatory_code no _item_type.code text _item_examples.case ; The ensemble has a slight translation between domains 1 and 4, but overall it can accurately be described as point group 222 ; save_ save__struct_ncs_ens.id _item_description.description ; The value of _struct_ncs_ens.id must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_ens.id' struct_ncs_ens yes '_struct_ncs_ens_gen.ens_id' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens.id' _item_type.code code save_ save__struct_ncs_ens.point_group _item_description.description ; The point group of the ensemble of structural elements related by one or more noncrystallographic symmetry operations. The relationships need not be precise; this data item is intended to give a rough description of the noncrystallographic symmetry relationships. ; _item.name '_struct_ncs_ens.point_group' _item.category_id struct_ncs_ens _item.mandatory_code no _item_type.code line loop_ _item_examples.case '3' '422' 'non-proper' save_ ######################## ## STRUCT_NCS_ENS_GEN ## ######################## save_struct_ncs_ens_gen _category.description ; Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator. ; _category.id struct_ncs_ens_gen _category.mandatory_code no loop_ _category_key.name '_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_ens_gen.oper_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the collagen-like peptide, HYP-. ; ; _struct_ncs_ens_gen.dom_id_1 d1 _struct_ncs_ens_gen.dom_id_2 d2 _struct_ncs_ens_gen.ens_id en1 _struct_ncs_ens_gen.oper_id ncsop1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_ens_gen.dom_id_1 _item_description.description ; The identifier for the domain that will remain unchanged by the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_struct_ncs_ens_gen.dom_id_1' _item.mandatory_code yes save_ save__struct_ncs_ens_gen.dom_id_2 _item_description.description ; The identifier for the domain that will be transformed by application of the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category. ; _item.name '_struct_ncs_ens_gen.dom_id_2' _item.mandatory_code yes save_ save__struct_ncs_ens_gen.ens_id _item_description.description ; This data item is a pointer to _struct_ncs_ens.id in the STRUCT_NCS_ENS category. ; _item.name '_struct_ncs_ens_gen.ens_id' _item.mandatory_code yes save_ save__struct_ncs_ens_gen.oper_id _item_description.description ; This data item is a pointer to _struct_ncs_oper.id in the STRUCT_NCS_OPER category. ; _item.name '_struct_ncs_ens_gen.oper_id' _item.mandatory_code yes save_ ##################### ## STRUCT_NCS_OPER ## ##################### save_struct_ncs_oper _category.description ; Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations. ; _category.id struct_ncs_oper _category.mandatory_code no _category_key.name '_struct_ncs_oper.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for the protein NS1. ; ; _struct_ncs_oper.id ncsop1 _struct_ncs_oper.code given _struct_ncs_oper.matrix[1][1] 0.247 _struct_ncs_oper.matrix[1][2] 0.935 _struct_ncs_oper.matrix[1][3] 0.256 _struct_ncs_oper.matrix[2][1] 0.929 _struct_ncs_oper.matrix[2][2] 0.153 _struct_ncs_oper.matrix[2][3] 0.337 _struct_ncs_oper.matrix[3][1] 0.276 _struct_ncs_oper.matrix[3][2] 0.321 _struct_ncs_oper.matrix[3][3] -0.906 _struct_ncs_oper.vector[1] -8.253 _struct_ncs_oper.vector[2] -11.743 _struct_ncs_oper.vector[3] -1.782 _struct_ncs_oper.details ; Matrix and translation vector for pseudo-twofold operation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ncs_oper.code _item_description.description ; A code to indicate whether this operator describes a relationship between coordinates all of which are given in the data block (in which case the value of code is 'given'), or whether the operator is used to generate new coordinates from those that are given in the data block (in which case the value of code is 'generate'). ; _item.name '_struct_ncs_oper.code' _item.category_id struct_ncs_oper _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail given ; operator relates coordinates given in the data block ; generate ; operator generates new coordinates from those given in the data block ; save_ save__struct_ncs_oper.details _item_description.description ; A description of special aspects of the noncrystallographic symmetry operator. ; _item.name '_struct_ncs_oper.details' _item.category_id struct_ncs_oper _item.mandatory_code no _item_type.code text _item_examples.case ; The operation is given as a precise threefold rotation, despite the fact the best rms fit between domain 1 and domain 2 yields a rotation of 119.7 degrees and a translation of 0.13 angstroms. ; save_ save__struct_ncs_oper.id _item_description.description ; The value of _struct_ncs_oper.id must uniquely identify a record in the STRUCT_NCS_OPER list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ncs_oper.id' struct_ncs_oper yes '_struct_ncs_ens_gen.oper_id' struct_ncs_ens_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ncs_ens_gen.oper_id' '_struct_ncs_oper.id' _item_type.code code save_ save__struct_ncs_oper.matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[1][1]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[1][2]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[1][3]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[2][1]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[2][2]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[2][3]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[3][1]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[3][2]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.matrix[3][3]' _item.category_id struct_ncs_oper _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_ncs_oper.vector[1] _item_description.description ; The [1] element of the three-element vector component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.vector[1]' _item.category_id struct_ncs_oper _item.mandatory_code no # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__struct_ncs_oper.vector[2] _item_description.description ; The [2] element of the three-element vector component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.vector[2]' _item.category_id struct_ncs_oper _item.mandatory_code no # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__struct_ncs_oper.vector[3] _item_description.description ; The [3] element of the three-element vector component of a noncrystallographic symmetry operation. ; _item.name '_struct_ncs_oper.vector[3]' _item.category_id struct_ncs_oper _item.mandatory_code no # _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ################ ## STRUCT_REF ## ################ save_struct_ref _category.description ; Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category. ; _category.id struct_ref _category.mandatory_code no _category_key.name '_struct_ref.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.biol_id _struct_ref.db_name _struct_ref.db_code _struct_ref.seq_align _struct_ref.seq_dif _struct_ref.details 1 1 . 'Genbank' '12345' 'entire' 'yes' . 2 . 2 'PDB' '1ABC' . . ; The structure of the closely related compound, isobutyryl-pepstatin (pepstatin A) in complex with rhizopuspepsin ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref.biol_id _item_description.description ; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category. ; _item.name '_struct_ref.biol_id' _item.mandatory_code no save_ save__struct_ref.db_code _item_description.description ; The code for this entity or biological unit or for a closely related entity or biological unit in the named database. ; _item.name '_struct_ref.db_code' _item.category_id struct_ref _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '1ABC' 'ABCDEF' save_ save__struct_ref.db_name _item_description.description ; The name of the database containing reference information about this entity or biological unit. ; _item.name '_struct_ref.db_name' _item.category_id struct_ref _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'PDB' 'CSD' 'Genbank' save_ save__struct_ref.details _item_description.description ; A description of special aspects of the relationship between the entity or biological unit described in the data block and that in the referenced database entry. ; _item.name '_struct_ref.details' _item.category_id struct_ref _item.mandatory_code no _item_type.code text save_ save__struct_ref.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_struct_ref.entity_id' _item.mandatory_code yes save_ save__struct_ref.id _item_description.description ; The value of _struct_ref.id must uniquely identify a record in the STRUCT_REF list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ref.id' struct_ref yes '_struct_ref_seq.ref_id' struct_ref_seq yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ref_seq.ref_id' '_struct_ref.id' _item_type.code code save_ save__struct_ref.seq_align _item_description.description ; A flag to indicate the scope of the alignment between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. 'entire' indicates that alignment spans the entire length of both sequences (although point differences may occur and can be annotated using the data items in the STRUCT_REF_SEQ_DIF category). 'partial' indicates a partial alignment. The region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. This data item may also take the value '.', indicating that the reference is not to a sequence. ; _item.name '_struct_ref.seq_align' _item.category_id struct_ref _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail complete 'alignment is complete' partial 'alignment is partial' . 'reference is not to a sequence' save_ save__struct_ref.seq_dif _item_description.description ; A flag to indicate the presence ('yes') or absence ('no') of point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item may also take the value '.', indicating that the reference is not to a sequence. ; _item.name '_struct_ref.seq_dif' _item.category_id struct_ref _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'there are no point differences' n 'abbreviation for "no"' yes 'there are point difference' y 'abbreviation for "yes"' . 'reference is not to a sequence' save_ #################### ## STRUCT_REF_SEQ ## #################### save_struct_ref_seq _category.description ; Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry. ; _category.id struct_ref_seq _category.mandatory_code no _category_key.name '_struct_ref_seq.align_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on the sequence alignment of CHER from M. xantus (36 to 288) and CHER from S. typhimurium (18 to 276). ; ; _struct_ref_seq.align_id alg1 _struct_ref_seq.ref_id seqdb1 _struct_ref_seq.seq_align_beg 36 _struct_ref_seq.seq_align_end 288 _struct_ref_seq.db_align_beg 18 _struct_ref_seq.db_align_end 276 _struct_ref_seq.details ; The alignment contains 3 gaps larger than 2 residues ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref_seq.align_id _item_description.description ; The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ref_seq.align_id' struct_ref_seq yes '_struct_ref_seq_dif.align_id' struct_ref_seq_dif yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ref_seq_dif.align_id' '_struct_ref_seq.align_id' _item_type.code code save_ save__struct_ref_seq.db_align_beg _item_description.description ; The sequence position in the referenced database entry at which the alignment begins. ; _item.name '_struct_ref_seq.db_align_beg' _item.mandatory_code yes # loop_ # _item_range.maximum # _item_range.minimum . 1 # 1 1 _item_type.code int save_ save__struct_ref_seq.db_align_end _item_description.description ; The sequence position in the referenced database entry at which the alignment ends. ; _item.name '_struct_ref_seq.db_align_end' _item.mandatory_code yes # loop_ # _item_range.maximum # _item_range.minimum . 1 # 1 1 _item_type.code int save_ save__struct_ref_seq.details _item_description.description ; A description of special aspects of the sequence alignment. ; _item.name '_struct_ref_seq.details' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code text save_ save__struct_ref_seq.ref_id _item_description.description ; This data item is a pointer to _struct_ref.id in the STRUCT_REF category. ; _item.name '_struct_ref_seq.ref_id' _item.mandatory_code yes save_ save__struct_ref_seq.seq_align_beg _item_description.description ; The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq.seq_align_beg' _item.mandatory_code yes save_ save__struct_ref_seq.seq_align_end _item_description.description ; The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq.seq_align_end' _item.mandatory_code yes save_ ######################## ## STRUCT_REF_SEQ_DIF ## ######################## save_struct_ref_seq_dif _category.description ; Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry. ; _category.id struct_ref_seq_dif _category.mandatory_code no loop_ _category_key.name '_struct_ref_seq_dif.align_id' '_struct_ref_seq_dif.seq_num' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on laboratory records for CAP-DNA complex. ; ; _struct_ref_seq_dif.align_id algn2 _struct_ref_seq_dif.seq_num 181 _struct_ref_seq_dif.db_mon_id GLU _struct_ref_seq_dif.mon_id PHE _struct_ref_seq_dif.details ; A point mutation was introduced in the CAP at position 181 substituting PHE for GLU. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref_seq_dif.align_id _item_description.description ; This data item is a pointer to _struct_ref_seq.align_id in the STRUCT_REF_SEQ category. ; _item.name '_struct_ref_seq_dif.align_id' _item.mandatory_code yes save_ save__struct_ref_seq_dif.db_mon_id _item_description.description ; The monomer type found at this position in the referenced database entry. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_ref_seq_dif.db_mon_id' _item.mandatory_code yes save_ save__struct_ref_seq_dif.details _item_description.description ; A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. ; _item.name '_struct_ref_seq_dif.details' _item.category_id struct_ref_seq_dif _item.mandatory_code no _item_type.code text save_ save__struct_ref_seq_dif.mon_id _item_description.description ; The monomer type found at this position in the sequence of the entity or biological unit described in this data block. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_ref_seq_dif.mon_id' _item.mandatory_code yes save_ save__struct_ref_seq_dif.seq_num _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq_dif.seq_num' _item.mandatory_code yes save_ ################## ## STRUCT_SHEET ## ################## save_struct_sheet _category.description ; Data items in the STRUCT_SHEET category record details about the beta-sheets. ; _category.id struct_sheet _category.mandatory_code no _category_key.name '_struct_sheet.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. N O N O N O N O N O N O 10--11--12--13--14--15--16--17--18--19--20 strand_a N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 30--31--32--33--34--35--36--37--38--39--40 strand_b N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 50--51--52--53--54--55--56--57--58--59--60 strand_c N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 70--71--72--73--74--75--76--77--78--79--80 strand_d N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 90--91--92--93--94--95--96--97--98--99-100 strand_e N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 110-111-112-113-114-115-116-117-118-119-120 strand_f N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 130-131-132-133-134-135-136-137-138-139-140 strand_g N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 150-151-152-153-154-155-156-157-158-159-160 strand_h N O N O N O N O N O / \ / \ / \ / \ / \ ; ; _struct_sheet.id sheet_1 _struct_sheet.type 'beta-barrel' _struct_sheet.number_strands 8 _struct_sheet.details . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. N O N O N O N O -10--11--12--13--14--15--16--17--18-> strand_a N O N O N O N O N O | | | | | | | | | | O N O N O N O N O N <-119-118-117-116-115-114-113-112-111-110- strand_b O N O N O N O N O N \ / \ / \ / \ / \ O N O N O N O N O N O N <-41--40--39--38--37--36--35--34--33--32--31--30- strand_c O N O N O N O N O N O N | | | | | | | | | | | | N O N O N O N O N O N O strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2 N O N O N O N O N O | | | | | | | | | | | | O N O N O N O N O N O N <-80--79--78--77--76--75--74--73--72--71--70- strand_e O N O N O N O N O N ; ; _struct_sheet.id sheet_2 _struct_sheet.type 'five stranded, mixed-sense' _struct_sheet.number_strands 5 _struct_sheet.details 'strand_d is in two pieces' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet.details _item_description.description ; A description of special aspects of the beta-sheet. ; _item.name '_struct_sheet.details' _item.category_id struct_sheet _item.mandatory_code no _item_type.code text save_ save__struct_sheet.id _item_description.description ; The value of _struct_sheet.id must uniquely identify a record in the STRUCT_SHEET list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_sheet.id' struct_sheet yes '_struct_sheet_hbond.sheet_id' struct_sheet_hbond yes '_struct_sheet_order.sheet_id' struct_sheet_order yes '_struct_sheet_range.sheet_id' struct_sheet_range yes '_struct_sheet_topology.sheet_id' struct_sheet_topology yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_sheet_hbond.sheet_id' '_struct_sheet.id' '_struct_sheet_order.sheet_id' '_struct_sheet.id' '_struct_sheet_range.sheet_id' '_struct_sheet.id' '_struct_sheet_topology.sheet_id' '_struct_sheet.id' _item_type.code code save_ save__struct_sheet.number_strands _item_description.description ; The number of strands in the sheet. If a given range of residues bulges out from the strands, it is still counted as one strand. If a strand is composed of two different regions of polypeptide, it is still counted as one strand, as long as the proper hydrogen- bonding connections are made to adjacent strands. ; _item.name '_struct_sheet.number_strands' _item.category_id struct_sheet _item.mandatory_code no _item_type.code int save_ save__struct_sheet.type _item_description.description ; A simple descriptor for the type of the sheet. ; _item.name '_struct_sheet.type' _item.category_id struct_sheet _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'jelly-roll' 'Rossmann fold' 'beta barrel' save_ ######################## ## STRUCT_SHEET_HBOND ## ######################## save_struct_sheet_hbond _category.description ; Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet. ; _category.id struct_sheet_hbond _category.mandatory_code no loop_ _category_key.name '_struct_sheet_hbond.sheet_id' '_struct_sheet_hbond.range_id_1' '_struct_sheet_hbond.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_hbond.sheet_id _struct_sheet_hbond.range_id_1 _struct_sheet_hbond.range_id_2 _struct_sheet_hbond.range_1_beg_label_seq_id _struct_sheet_hbond.range_1_beg_label_atom_id _struct_sheet_hbond.range_2_beg_label_seq_id _struct_sheet_hbond.range_2_beg_label_atom_id _struct_sheet_hbond.range_1_end_label_seq_id _struct_sheet_hbond.range_1_end_label_atom_id _struct_sheet_hbond.range_2_end_label_seq_id _struct_sheet_hbond.range_2_end_label_atom_id sheet_1 strand_a strand_b 11 N 30 O 19 O 40 N sheet_1 strand_b strand_c 31 N 50 O 39 O 60 N sheet_1 strand_c strand_d 51 N 70 O 59 O 80 N sheet_1 strand_d strand_e 71 N 90 O 89 O 100 N sheet_1 strand_e strand_f 91 N 110 O 99 O 120 N sheet_1 strand_f strand_g 111 N 130 O 119 O 140 N sheet_1 strand_g strand_h 131 N 150 O 139 O 160 N sheet_1 strand_h strand_a 151 N 10 O 159 O 180 N ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_hbond.sheet_id _struct_sheet_hbond.range_id_1 _struct_sheet_hbond.range_id_2 _struct_sheet_hbond.range_1_beg_label_seq_id _struct_sheet_hbond.range_1_beg_label_atom_id _struct_sheet_hbond.range_2_beg_label_seq_id _struct_sheet_hbond.range_2_beg_label_atom_id _struct_sheet_hbond.range_1_end_label_seq_id _struct_sheet_hbond.range_1_end_label_atom_id _struct_sheet_hbond.range_2_end_label_seq_id _struct_sheet_hbond.range_2_end_label_atom_id sheet_2 strand_a strand_b 20 N 119 O 18 O 111 N sheet_2 strand_b strand_c 110 N 33 O 118 N 41 O sheet_2 strand_c strand_d1 38 N 52 O 40 O 50 N sheet_2 strand_c strand_d2 30 N 96 O 36 O 90 N sheet_2 strand_d1 strand_e 51 N 80 O 51 O 80 N sheet_2 strand_d2 strand_e 91 N 76 O 97 O 70 N ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_hbond.range_1_beg_label_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_beg_label_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_end_label_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_end_label_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_beg_label_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_beg_label_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_end_label_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_label_atom_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_2_end_label_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_1_beg_auth_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_1_beg_auth_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_beg_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_1_end_auth_atom_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_1_end_auth_seq_id _item_description.description ; A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_1_end_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_beg_auth_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_beg_auth_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_beg_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_end_auth_atom_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_auth_atom_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_2_end_auth_seq_id _item_description.description ; A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_hbond.range_2_end_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_hbond.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_hbond.range_id_1' _item.mandatory_code yes save_ save__struct_sheet_hbond.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_hbond.range_id_2' _item.mandatory_code yes save_ save__struct_sheet_hbond.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_hbond.sheet_id' _item.mandatory_code yes save_ ######################## ## STRUCT_SHEET_ORDER ## ######################## save_struct_sheet_order _category.description ; Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described. ; _category.id struct_sheet_order _category.mandatory_code no loop_ _category_key.name '_struct_sheet_order.sheet_id' '_struct_sheet_order.range_id_1' '_struct_sheet_order.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense sheet_1 strand_a strand_b +1 parallel sheet_1 strand_b strand_c +1 parallel sheet_1 strand_c strand_d +1 parallel sheet_1 strand_d strand_e +1 parallel sheet_1 strand_e strand_f +1 parallel sheet_1 strand_f strand_g +1 parallel sheet_1 strand_g strand_h +1 parallel sheet_1 strand_h strand_a +1 parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense sheet_2 strand_a strand_b +1 anti-parallel sheet_2 strand_b strand_c +1 parallel sheet_2 strand_c strand_d1 +1 anti-parallel sheet_2 strand_c strand_d2 +1 anti-parallel sheet_2 strand_d1 strand_e +1 anti-parallel sheet_2 strand_d2 strand_e +1 anti-parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_order.offset _item_description.description ; Designates the relative position in the sheet, plus or minus, of the second residue range to the first. ; _item.name '_struct_sheet_order.offset' _item.category_id struct_sheet_order _item.mandatory_code no _item_type.code int save_ save__struct_sheet_order.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_order.range_id_1' _item.mandatory_code yes save_ save__struct_sheet_order.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_order.range_id_2' _item.mandatory_code yes save_ save__struct_sheet_order.sense _item_description.description ; A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. ; _item.name '_struct_sheet_order.sense' _item.category_id struct_sheet_order _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value 'parallel' 'anti-parallel' save_ save__struct_sheet_order.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_order.sheet_id' _item.mandatory_code yes save_ ######################## ## STRUCT_SHEET_RANGE ## ######################## save_struct_sheet_range _category.description ; Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range. ; _category.id struct_sheet_range _category.mandatory_code no loop_ _category_key.name '_struct_sheet_range.sheet_id' '_struct_sheet_range.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.symmetry sheet_1 strand_a ala A 20 ala A 30 1_555 sheet_1 strand_b ala A 40 ala A 50 1_555 sheet_1 strand_c ala A 60 ala A 70 1_555 sheet_1 strand_d ala A 80 ala A 90 1_555 sheet_1 strand_e ala A 100 ala A 110 1_555 sheet_1 strand_f ala A 120 ala A 130 1_555 sheet_1 strand_g ala A 140 ala A 150 1_555 sheet_1 strand_h ala A 160 ala A 170 1_555 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.symmetry sheet_2 strand_a ala A 10 ala A 18 1_555 sheet_2 strand_b ala A 110 ala A 119 1_555 sheet_2 strand_c ala A 30 ala A 41 1_555 sheet_2 strand_d1 ala A 50 ala A 52 1_555 sheet_2 strand_d2 ala A 90 ala A 97 1_555 sheet_2 strand_e ala A 70 ala A 80 1_555 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_range.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_struct_sheet_range.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_sheet_range.beg_label_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_sheet_range.beg_label_comp_id' _item.mandatory_code yes save_ save__struct_sheet_range.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_range.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_struct_sheet_range.end_label_asym_id' _item.mandatory_code yes save_ save__struct_sheet_range.end_label_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_struct_sheet_range.end_label_comp_id' _item.mandatory_code yes save_ save__struct_sheet_range.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_label_seq_id' _item.mandatory_code yes save_ save__struct_sheet_range.beg_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_sheet_range.beg_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_sheet_range.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_range.end_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_auth_asym_id' _item.mandatory_code no save_ save__struct_sheet_range.end_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_auth_comp_id' _item.mandatory_code no save_ save__struct_sheet_range.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_sheet_range.end_auth_seq_id' _item.mandatory_code no save_ save__struct_sheet_range.id _item_description.description ; The value of _struct_sheet_range.id must uniquely identify a range in a given sheet in the STRUCT_SHEET_RANGE list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_sheet_range.id' struct_sheet_range yes '_struct_sheet_hbond.range_id_1' struct_sheet_hbond yes '_struct_sheet_hbond.range_id_2' struct_sheet_hbond yes '_struct_sheet_order.range_id_1' struct_sheet_order yes '_struct_sheet_order.range_id_2' struct_sheet_order yes '_struct_sheet_topology.range_id_1' struct_sheet_topology yes '_struct_sheet_topology.range_id_2' struct_sheet_topology yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_sheet_hbond.range_id_1' '_struct_sheet_range.id' '_struct_sheet_hbond.range_id_2' '_struct_sheet_range.id' '_struct_sheet_order.range_id_1' '_struct_sheet_range.id' '_struct_sheet_order.range_id_2' '_struct_sheet_range.id' '_struct_sheet_topology.range_id_1' '_struct_sheet_range.id' '_struct_sheet_topology.range_id_2' '_struct_sheet_range.id' _item_type.code code save_ save__struct_sheet_range.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_range.sheet_id' _item.mandatory_code yes save_ save__struct_sheet_range.symmetry _item_description.description ; Describes the symmetry operation that should be applied to the residues delimited by the start and end designators in order to generate the appropriate strand in this sheet. ; _item.name '_struct_sheet_range.symmetry' _item.category_id struct_sheet_range _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop save_ ########################### ## STRUCT_SHEET_TOPOLOGY ## ########################### save_struct_sheet_topology _category.description ; Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets. ; _category.id struct_sheet_topology _category.mandatory_code no loop_ _category_key.name '_struct_sheet_topology.sheet_id' '_struct_sheet_topology.range_id_1' '_struct_sheet_topology.range_id_2' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - simple beta-barrel. ; ; loop_ _struct_sheet_topology.sheet_id _struct_sheet_topology.range_id_1 _struct_sheet_topology.range_id_2 _struct_sheet_topology.offset _struct_sheet_topology.sense sheet_1 strand_a strand_b +1 parallel sheet_1 strand_b strand_c +1 parallel sheet_1 strand_c strand_d +1 parallel sheet_1 strand_d strand_e +1 parallel sheet_1 strand_e strand_f +1 parallel sheet_1 strand_f strand_g +1 parallel sheet_1 strand_g strand_h +1 parallel sheet_1 strand_h strand_a +1 parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - five stranded mixed-sense sheet with one two-piece strand. ; ; loop_ _struct_sheet_topology.sheet_id _struct_sheet_topology.range_id_1 _struct_sheet_topology.range_id_2 _struct_sheet_topology.offset _struct_sheet_topology.sense sheet_2 strand_a strand_c +2 anti-parallel sheet_2 strand_c strand_d1 +1 anti-parallel sheet_2 strand_d1 strand_e +1 anti-parallel sheet_2 strand_e strand_d2 -1 anti-parallel sheet_2 strand_d2 strand_b -2 anti-parallel ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_sheet_topology.offset _item_description.description ; Designates the relative position in the sheet, plus or minus, of the second residue range to the first. ; _item.name '_struct_sheet_topology.offset' _item.category_id struct_sheet_topology _item.mandatory_code no _item_type.code int save_ save__struct_sheet_topology.range_id_1 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_topology.range_id_1' _item.mandatory_code yes save_ save__struct_sheet_topology.range_id_2 _item_description.description ; This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category. ; _item.name '_struct_sheet_topology.range_id_2' _item.mandatory_code yes save_ save__struct_sheet_topology.sense _item_description.description ; A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. ; _item.name '_struct_sheet_topology.sense' _item.category_id struct_sheet_topology _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value 'parallel' 'anti-parallel' save_ save__struct_sheet_topology.sheet_id _item_description.description ; This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category. ; _item.name '_struct_sheet_topology.sheet_id' _item.mandatory_code yes save_ ################# ## STRUCT_SITE ## ################# save_struct_site _category.description ; Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites). ; _category.id struct_site _category.mandatory_code no _category_key.name '_struct_site.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_site.id _struct_site.details 'P2 site C' ; residues with a contact < 3.7 \%A to an atom in the P2 moiety of the inhibitor in the conformation with _struct_asym.id = C ; 'P2 site D' ; residues with a contact < 3.7 \%A to an atom in the P1 moiety of the inhibitor in the conformation with _struct_asym.id = D) ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site.details _item_description.description ; A description of special aspects of the site. ; _item.name '_struct_site.details' _item.category_id struct_site _item.mandatory_code no _item_type.code text save_ save__struct_site.id _item_description.description ; The value of _struct_site.id must uniquely identify a record in the STRUCT_SITE list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_site.id' struct_site yes '_struct_site_gen.site_id' struct_site_gen yes '_struct_site_keywords.site_id' struct_site_keywords yes '_struct_site_view.site_id' struct_site_view yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_site_gen.site_id' '_struct_site.id' '_struct_site_keywords.site_id' '_struct_site.id' '_struct_site_view.site_id' '_struct_site.id' _item_type.code line save_ ##################### ## STRUCT_SITE_GEN ## ##################### save_struct_site_gen _category.description ; Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites. ; _category.id struct_site_gen _category.mandatory_code no loop_ _category_key.name '_struct_site_gen.id' '_struct_site_gen.site_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.symmetry _struct_site_gen.details 1 1 VAL A 32 1_555 . 2 1 ILE A 47 1_555 . 3 1 VAL A 82 1_555 . 4 1 ILE A 84 1_555 . 5 2 VAL B 232 1_555 . 6 2 ILE B 247 1_555 . 7 2 VAL B 282 1_555 . 8 2 ILE B 284 1_555 . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site_gen.details _item_description.description ; A description of special aspects of the symmetry generation of this portion of the structural site. ; _item.name '_struct_site_gen.details' _item.category_id struct_site_gen _item.mandatory_code no _item_type.code text _item_examples.case ; The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. ; save_ save__struct_site_gen.id _item_description.description ; The value of _struct_site_gen.id must uniquely identify a record in the STRUCT_SITE_GEN list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_site_gen.id' _item.category_id struct_site_gen _item.mandatory_code yes _item_type.code line save_ save__struct_site_gen.label_alt_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_struct_site_gen.label_alt_id' _item.mandatory_code yes save_ save__struct_site_gen.label_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.label_asym_id' _item.mandatory_code yes save_ save__struct_site_gen.label_atom_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_struct_site_gen.label_atom_id' _item.mandatory_code yes save_ save__struct_site_gen.label_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.label_comp_id' _item.mandatory_code yes save_ save__struct_site_gen.label_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.label_seq_id' _item.mandatory_code yes save_ save__struct_site_gen.auth_asym_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_asym_id' _item.mandatory_code no save_ save__struct_site_gen.auth_atom_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_atom_id' _item.mandatory_code no save_ save__struct_site_gen.auth_comp_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_comp_id' _item.mandatory_code no save_ save__struct_site_gen.auth_seq_id _item_description.description ; A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_site_gen.auth_seq_id' _item.mandatory_code no save_ save__struct_site_gen.site_id _item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ; _item.name '_struct_site_gen.site_id' _item.mandatory_code yes save_ save__struct_site_gen.symmetry _item_description.description ; Describes the symmetry operation that should be applied to the atom set specified by _struct_site_gen.label* to generate a portion of the site. ; _item.name '_struct_site_gen.symmetry' _item.category_id struct_site_gen _item.mandatory_code no # _item_default.value 1_555 _item_type.code symop loop_ _item_examples.case _item_examples.detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' save_ ########################## ## STRUCT_SITE_KEYWORDS ## ########################## save_struct_site_keywords _category.description ; Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site. ; _category.id struct_site_keywords _category.mandatory_code no loop_ _category_key.name '_struct_site_keywords.site_id' '_struct_site_keywords.text' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _struct_site_keywords.site_id _struct_site_keywords.text 'P2 site C' 'binding site' 'P2 site C' 'binding pocket' 'P2 site C' 'P2 site' 'P2 site C' 'P2 pocket' 'P2 site D' 'binding site' 'P2 site D' 'binding pocket' 'P2 site D' 'P2 site' 'P2 site D' 'P2 pocket' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site_keywords.site_id _item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ; _item.name '_struct_site_keywords.site_id' _item.mandatory_code yes save_ save__struct_site_keywords.text _item_description.description ; Keywords describing this site. ; _item.name '_struct_site_keywords.text' _item.category_id struct_site_keywords _item.mandatory_code yes _item_type.code text loop_ _item_examples.case 'active site' 'binding pocket' 'Ca coordination' save_ ###################### ## STRUCT_SITE_VIEW ## ###################### save_struct_site_view _category.description ; Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site. ; _category.id struct_site_view _category.mandatory_code no _category_key.name '_struct_site_view.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry (1989), 28, 310-320]. ; ; _struct_site_view.id 1 _struct_site_view.rot_matrix[1][1] 0.132 _struct_site_view.rot_matrix[1][2] 0.922 _struct_site_view.rot_matrix[1][3] -0.363 _struct_site_view.rot_matrix[2][1] 0.131 _struct_site_view.rot_matrix[2][2] -0.380 _struct_site_view.rot_matrix[2][3] -0.916 _struct_site_view.rot_matrix[3][1] -0.982 _struct_site_view.rot_matrix[3][2] 0.073 _struct_site_view.rot_matrix[3][3] -0.172 _struct_site_view.details ; This view highlights the site of ATAT-Netropsin interaction. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_site_view.details _item_description.description ; A description of special aspects of this view of the site. This data item can be used as a figure legend. ; _item.name '_struct_site_view.details' _item.category_id struct_site_view _item.mandatory_code no _item_type.code text _item_examples.case ; The active site has been oriented with the specificity pocket on the right and the active site machinery on the left. ; save_ save__struct_site_view.id _item_description.description ; The value of _struct_site_view.id must uniquely identify a record in the STRUCT_SITE_VIEW list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_site_view.id' _item.category_id struct_site_view _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Figure 1' 'unliganded enzyme' 'view down enzyme active site' save_ save__struct_site_view.rot_matrix[1][1] _item_description.description ; The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[1][1]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[1][2] _item_description.description ; The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[1][2]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[1][3] _item_description.description ; The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[1][3]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[2][1] _item_description.description ; The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[2][1]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[2][2] _item_description.description ; The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[2][2]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[2][3] _item_description.description ; The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[2][3]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[3][1] _item_description.description ; The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[3][1]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[3][2] _item_description.description ; The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[3][2]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.rot_matrix[3][3] _item_description.description ; The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| ; _item.name '_struct_site_view.rot_matrix[3][3]' _item.category_id struct_site_view _item.mandatory_code no _item_sub_category.id matrix _item_type.code float save_ save__struct_site_view.site_id _item_description.description ; This data item is a pointer to _struct_site.id in the STRUCT_SITE category. ; _item.name '_struct_site_view.site_id' _item.mandatory_code yes save_ ############## ## SYMMETRY ## ############## save_symmetry _category.description ; Data items in the SYMMETRY category record details about the space-group symmetry. ; _category.id symmetry _category.mandatory_code no _category_key.name '_symmetry.entry_id' loop_ _category_group.id 'inclusive_group' 'symmetry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; _symmetry.entry_id '5HVP' _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_H-M 'P 21 21 2' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__symmetry.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_symmetry.entry_id' _item.mandatory_code yes save_ save__symmetry.cell_setting _item_description.description ; The cell settings for this space-group symmetry. ; _item.name '_symmetry.cell_setting' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_cell_setting' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code ucode loop_ _item_enumeration.value triclinic monoclinic orthorhombic tetragonal rhombohedral trigonal hexagonal cubic save_ save__symmetry.Int_Tables_number _item_description.description ; Space-group number from International Tables for Crystallography Vol. A (2002). ; _item.name '_symmetry.Int_Tables_number' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_Int_Tables_number' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ save__symmetry.space_group_name_Hall _item_description.description ; Space-group symbol as described by Hall (1981). This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981) A37, 921. ; _item.name '_symmetry.space_group_name_Hall' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_space_group_name_Hall' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case '-P 2ac 2n' '-R 3 2"' 'P 61 2 2 (0 0 -1)' save_ save__symmetry.space_group_name_H-M _item_description.description ; Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv.pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes. ; _item.name '_symmetry.space_group_name_H-M' _item.category_id symmetry _item.mandatory_code no _item_aliases.alias_name '_symmetry_space_group_name_H-M' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'P 1 21/m 1' 'P 2/n 2/n 2/n (origin at -1)' 'R -3 2/m' save_ #################### ## SYMMETRY_EQUIV ## #################### save_symmetry_equiv _category.description ; Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group. ; _category.id symmetry_equiv _category.mandatory_code no _category_key.name '_symmetry_equiv.id' loop_ _category_group.id 'inclusive_group' 'symmetry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. ; ; loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 '+x,+y,+z' 2 '-x,-y,z' 3 '1/2+x,1/2-y,-z' 4 '1/2-x,1/2+y,-z' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__symmetry_equiv.id _item_description.description ; The value of _symmetry_equiv.id must uniquely identify a record in the SYMMETRY_EQUIV category. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_symmetry_equiv.id' _item.category_id symmetry_equiv _item.mandatory_code yes _item_aliases.alias_name '_symmetry_equiv_pos_site_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__symmetry_equiv.pos_as_xyz _item_description.description ; Symmetry-equivalent position in the 'xyz' representation. Except for the space group P1, these data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography Vol. A (2002). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. ; _item.name '_symmetry_equiv.pos_as_xyz' _item.category_id symmetry_equiv _item.mandatory_code no _item_aliases.alias_name '_symmetry_equiv_pos_as_xyz' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '-y+x,-y,1/3+z' save_ ### EOF mmcif_std-def-1.dic ########################################################################### # # File: mmcif_std-def-2.dic # # mmCIF Data Dictionary # # This data dictionary contains the standard mmCIF data definitions. # # Definition Section 2 # # Section 2 contains definitions added to maintain correspondence # with the Core CIF dictionary V2.3 # # # ########################################################################### save__atom_site.adp_type _item_description.description ; A standard code used to describe the type of atomic displacement parameters used for the site. ; _item.name '_atom_site.adp_type' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.thermal_displace_type' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_adp_type' cif_core.dic 2.3 save_ save__atom_site.refinement_flags _item_description.description ; A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by _atom_site.refinement_flags_posn, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs. ; _item.name '_atom_site.refinement_flags' _item.category_id atom_site _item.mandatory_code no _item_type.code code loop_ _item_related.related_name _item_related.function_code '_atom_site.refinement_flags_posn' replaces '_atom_site.refinement_flags_adp' replaces '_atom_site.refinement_flags_occupancy' replaces loop_ _item_enumeration.value _item_enumeration.detail . 'no refinement constraints' S 'special-position constraint on site' G 'rigid-group refinement of site' R 'riding-atom site attached to non-riding atom' D 'distance or angle restraint on site' T 'thermal displacement constraints' U 'Uiso or Uij restraint (rigid bond)' P 'partial occupancy constraint' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags' cif_core.dic 2.3 save_ save__atom_site.refinement_flags_adp _item_description.description ; A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site. ; _item.name '_atom_site.refinement_flags_adp' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.refinement_flags_posn' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail . 'no constraints on atomic displacement parameters' T 'special-position constraints on atomic displacement parameters' U 'Uiso or Uij restraint (rigid bond)' TU 'both constraints applied' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags_adp' cif_core.dic 2.3 save_ save__atom_site.refinement_flags_occupancy _item_description.description ; A code which indicates that refinement restraints or constraints were applied to the occupancy of this site. ; _item.name '_atom_site.refinement_flags_occupancy' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.refinement_flags_posn' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail . 'no constraints on site-occupancy parameters' P 'site-occupancy constraint' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags_occupancy' cif_core.dic 2.3 save_ save__atom_site.refinement_flags_posn _item_description.description ; A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site. ; _item.name '_atom_site.refinement_flags_posn' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_related.related_name '_atom_site.refinement_flags_posn' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail . 'no constraints on positional coordinates' D 'distance or angle restraint on positional coordinates' G 'rigid-group refinement of positional coordinates' R 'riding-atom site attached to non-riding atom' S 'special-position constraint on positional coordinates' DG 'combination of the above constraints' DR 'combination of the above constraints' DS 'combination of the above constraints' GR 'combination of the above constraints' GS 'combination of the above constraints' RS 'combination of the above constraints' DGR 'combination of the above constraints' DGS 'combination of the above constraints' DRS 'combination of the above constraints' GRS 'combination of the above constraints' DGRS 'combination of the above constraints' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_site_refinement_flags_posn' cif_core.dic 2.3 save_ save__atom_sites.special_details _item_description.description ; Additional information about the atomic coordinates not coded elsewhere in the CIF. ; _item.name '_atom_sites.special_details' _item.category_id atom_sites _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_sites_special_details' cif_core.dic 2.3 save_ save__atom_type.scat_dispersion_source _item_description.description ; Reference to the source of the real and imaginary dispersion corrections for scattering factors used for this atom type. ; _item.name '_atom_type.scat_dispersion_source' _item.category_id atom_type _item.mandatory_code no _item_type.code text _item_examples.case 'International Tables Vol. IV Table 2.3.1' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_atom_type_scat_dispersion_source' cif_core.dic 2.3 save_ ################ ## AUDIT_LINK ## ################ save_audit_link _category.description ; Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF. ; _category.id 'audit_link' _category.mandatory_code no loop_ _category_key.name '_audit_link.block_code' '_audit_link.block_description' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_link.block_code _audit_link.block_description . 'discursive text of paper with two structures' morA_(1) 'structure 1 of 2' morA_(2) 'structure 2 of 2' ; ; Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _audit_link.block_code _audit_link.block_description . 'publication details' KSE_COM 'experimental data common to ref./mod. structures' KSE_REF 'reference structure' KSE_MOD 'modulated structure' ; ; Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_link.block_code _item_description.description ; The value of _audit_block.code associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness. ; _item.name '_audit_link.block_code' _item.category_id audit_link _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_audit_link_block_code' cif_core.dic 2.3 save_ save__audit_link.block_description _item_description.description ; A textual description of the relationship of the referenced data block to the current one. ; _item.name '_audit_link.block_description' _item.category_id audit_link _item.mandatory_code yes _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_audit_link_block_description' cif_core.dic 2.3 save_ ## save__cell.reciprocal_angle_alpha _item_description.description ; The angle (recip-alpha) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_angle_alpha' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 180.0 180.0 180.0 _item_default.value 90.0 _item_type_conditions.code esd _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_alpha_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_angle_alpha' cif_core.dic 2.3 save_ save__cell.reciprocal_angle_beta _item_description.description ; The angle (recip-beta) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_angle_beta' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 180.0 180.0 180.0 _item_default.value 90.0 _item_type_conditions.code esd _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_beta_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_angle_beta' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_gamma _item_description.description ; The angle (recip-gamma) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_angle_gamma' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 180.0 180.0 180.0 _item_default.value 90.0 _item_type_conditions.code esd _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_gamma_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_angle_gamma' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_alpha_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_angle_alpha. ; _item.name '_cell.reciprocal_angle_alpha_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_alpha' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_angle_alpha_esd' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_beta_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_angle_beta. ; _item.name '_cell.reciprocal_angle_beta_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_beta' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_angle_beta_esd' cif_core.dic 2.3 save_ # save__cell.reciprocal_angle_gamma_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_angle_gamma. ; _item.name '_cell.reciprocal_angle_gamma_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'degrees' _item_related.related_name '_cell.reciprocal_angle_gamma' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_angle_gamma_esd' cif_core.dic 2.3 save_ # save__cell.reciprocal_length_a _item_description.description ; The reciprocal cell length (recip-a) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_length_a' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'reciprocal_angstroms' _item_type_conditions.code esd _item_related.related_name '_cell.reciprocal_length_a_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_length_a' cif_core.dic 2.3 save_ save__cell.reciprocal_length_b _item_description.description ; The reciprocal cell length (recip-b) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_length_b' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'reciprocal_angstroms' _item_type_conditions.code esd _item_related.related_name '_cell.reciprocal_length_b_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_length_b' cif_core.dic 2.3 save_ save__cell.reciprocal_length_c _item_description.description ; The reciprocal cell length (recip-c) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. ; _item.name '_cell.reciprocal_length_c' _item.category_id cell _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'reciprocal_angstroms' _item_type_conditions.code esd _item_related.related_name '_cell.reciprocal_length_c_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_cell_reciprocal_length_c' cif_core.dic 2.3 save_ save__cell.reciprocal_length_a_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_length_a. ; _item.name '_cell.reciprocal_length_a_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'reciprocal_angstroms' _item_related.related_name '_cell.reciprocal_length_a' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_length_a_esd' cif_core.dic 2.3 save_ save__cell.reciprocal_length_b_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_length_b. ; _item.name '_cell.reciprocal_length_b_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'reciprocal_angstroms' _item_related.related_name '_cell.reciprocal_length_b' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_length_b_esd' cif_core.dic 2.3 save_ save__cell.reciprocal_length_c_esd _item_description.description ; The estimated standard deviation of _cell.reciprocal_length_c. ; _item.name '_cell.reciprocal_length_c_esd' _item.category_id cell _item.mandatory_code no _item_type.code float _item_units.code 'reciprocal_angstroms' _item_related.related_name '_cell.reciprocal_length_c' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_reciprocal_length_c_esd' cif_core.dic 2.3 save_ # save__cell.special_details # _item_description.description # ; A description of special aspects of the cell choice, noting # possible alternative settings. # ; # _item.name '_cell.special_details' # _item.category_id cell # _item.mandatory_code no # _item_type.code text # loop_ # _item_examples.case # 'pseudo-orthorhombic' # 'standard setting from 45 deg rotation around c' # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_cell_special_details' cif_core.dic 2.3 # save_ # # save__chemical.absolute_configuration _item_description.description ; Necessary conditions for the assignment of _chemical.absolute_configuration are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021) ; _item.name '_chemical.absolute_configuration' _item.category_id chemical _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail rm ; absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration ; ad ; absolute configuration established by anomalous-dispersion effects in diffraction measurements on the crystal ; rmad ; absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration and confirmed by anomalous-dispersion effects in diffraction measurements on the crystal ; syn ; absolute configuration has not been established by anomalous-dispersion effects in diffraction measurements on the crystal. The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure ; unk ; absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalous-dispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made ; . 'inapplicable' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_absolute_configuration' cif_core.dic 2.3 save_ save__chemical.melting_point_gt _item_description.description ; A temperature in kelvins above which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. _chemical.melting_point should always be used in preference to these two items whenever possible. ; _item.name '_chemical.melting_point_gt' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_related.related_name '_chemical.melting_point' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_melting_point_gt' cif_core.dic 2.3 save_ save__chemical.melting_point_lt _item_description.description ; A temperature in kelvins below which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. _chemical.melting_point should always be used in preference to these two items whenever possible. ; _item.name '_chemical.melting_point_lt' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_related.related_name '_chemical.melting_point' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_melting_point_lt' cif_core.dic 2.3 save_ save__chemical.optical_rotation _item_description.description ; The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent. ; _item.name '_chemical.optical_rotation' _item.category_id chemical _item.mandatory_code no _item_type.code line _item_examples.case '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_optical_rotation' cif_core.dic 2.3 save_ save__chemical.properties_biological _item_description.description ; A free-text description of the biological properties of the material. ; _item.name '_chemical.properties_biological' _item.category_id chemical _item.mandatory_code no _item_type.code text loop_ _item_examples.case ; diverse biological activities including use as a laxative and strong antibacterial activity against S. aureus and weak activity against cyclooxygenase-1 (COX-1) ; ; antibiotic activity against Bacillus subtilis (ATCC 6051) but no significant activity against Candida albicans (ATCC 14053), Aspergillus flavus (NRRL 6541) and Fusarium verticillioides (NRRL 25457) ; ; weakly potent lipoxygenase nonredox inhibitor ; ; no influenza A virus sialidase inhibitory and plaque reduction activities ; ; low toxicity against Drosophila melanogaster ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_properties_biological' cif_core.dic 2.3 save_ save__chemical.properties_physical _item_description.description ; A free-text description of the physical properties of the material. ; _item.name '_chemical.properties_physical' _item.category_id chemical _item.mandatory_code no _item_type.code text loop_ _item_examples.case air-sensitive moisture-sensitive hygroscopic deliquescent oxygen-sensitive photo-sensitive pyrophoric semiconductor 'ferromagnetic at low temperature' 'paramagnetic and thermochromic' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_properties_physical' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition _item_description.description ; The temperature in kelvins at which the solid decomposes. ; _item.name '_chemical.temperature_decomposition' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_examples.case 350 _item_related.related_name '_chemical.temperature_decomposition_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_decomposition' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition_esd _item_description.description ; The estimated standard deviation of _chemical.temperature_decomposition. ; _item.name '_chemical.temperature_decomposition_esd' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_related.related_name '_chemical.temperature_decomposition' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_chemical_temperature_decomposition_esd' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition_gt _item_description.description ; A temperature in kelvins above which the solid is known to decompose. _chemical.temperature_decomposition_gt and _chemical.temperature_decomposition_lt allow a range of temperatures to be given. _chemical.temperature_decomposition should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_decomposition_gt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_decomposition' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_decomposition_gt' cif_core.dic 2.3 save_ save__chemical.temperature_decomposition_lt _item_description.description ; A temperature in kelvins below which the solid is known to decompose. _chemical.temperature_decomposition_gt and _chemical.temperature_decomposition_lt allow a range of temperatures to be given. _chemical.temperature_decomposition should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_decomposition_lt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_decomposition' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_decomposition_lt' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation _item_description.description ; The temperature in kelvins at which the solid sublimes. ; _item.name '_chemical.temperature_sublimation' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_examples.case 350 _item_related.related_name '_chemical.temperature_sublimation_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_sublimation' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation_esd _item_description.description ; The estimated standard deviation of _chemical.temperature_sublimation. ; _item.name '_chemical.temperature_sublimation_esd' _item.category_id chemical _item.mandatory_code no _item_type.code float _item_units.code kelvins _item_related.related_name '_chemical.temperature_sublimation' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_chemical_temperature_sublimation_esd' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation_gt _item_description.description ; A temperature in kelvins above which the solid is known to sublime. _chemical.temperature_sublimation_gt and _chemical.temperature_sublimation_lt allow a range of temperatures to be given. _chemical.temperature_sublimation should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_sublimation_gt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_sublimation' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_sublimation_gt' cif_core.dic 2.3 save_ save__chemical.temperature_sublimation_lt _item_description.description ; A temperature in kelvins below which the solid is known to sublime. _chemical.temperature_sublimation_gt and _chemical.temperature_sublimation_lt allow a range of temperatures to be given. _chemical.temperature_sublimation should always be used in preference to these two items whenever possible. ; _item.name '_chemical.temperature_sublimation_lt' _item.category_id chemical _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_chemical.temperature_sublimation' _item_related.function_code alternate _item_examples.case 350 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_chemical_temperature_sublimation_lt' cif_core.dic 2.3 save_ # save__citation.database_id_CSD _item_description.description ; Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. ; _item.name '_citation.database_id_CSD' _item.category_id citation _item.mandatory_code no _item_type.code code _item_examples.case LEKKUH loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_citation_database_id_CSD' cif_core.dic 2.3 save_ save__database.CSD_history _item_description.description ; A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD). ; _item.name '_database.CSD_history' _item.category_id database _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_CSD_history' cif_core.dic 2.3 save_ save__database.code_CAS _item_description.description ; The code assigned by Chemical Abstracts. ; _item.name '_database.code_CAS' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_CAS' cif_core.dic 2.3 save_ save__database.code_CSD _item_description.description ; The code assigned by the Cambridge Structural Database. ; _item.name '_database.code_CSD' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_CSD' cif_core.dic 2.3 save_ save__database.code_ICSD _item_description.description ; The code assigned by the Inorganic Crystal Structure Database. ; _item.name '_database.code_ICSD' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_ICSD' cif_core.dic 2.3 save_ save__database.code_MDF _item_description.description ; The code assigned by the Metals Data File. ; _item.name '_database.code_MDF' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_MDF' cif_core.dic 2.3 save_ save__database.code_NBS _item_description.description ; The code assigned by the NBS (NIST) Crystal Data Database. ; _item.name '_database.code_NBS' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_NBS' cif_core.dic 2.3 save_ save__database.code_PDB _item_description.description ; The code assigned by the Protein Data Bank. ; _item.name '_database.code_PDB' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_PDB' cif_core.dic 2.3 save_ save__database.code_PDF _item_description.description ; The code assigned by the Powder Diffraction File (JCPDS/ICDD). ; _item.name '_database.code_PDF' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_PDF' cif_core.dic 2.3 save_ save__database.code_depnum_ccdc_fiz _item_description.description ; Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; _item.name '_database.code_depnum_ccdc_fiz' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_depnum_ccdc_fiz' cif_core.dic 2.3 save_ save__database.code_depnum_ccdc_journal _item_description.description ; Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; _item.name '_database.code_depnum_ccdc_journal' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_depnum_ccdc_journal' cif_core.dic 2.3 save_ save__database.code_depnum_ccdc_archive _item_description.description ; Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. ; _item.name '_database.code_depnum_ccdc_archive' _item.category_id database _item.mandatory_code no _item_type.code line loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_database_code_depnum_ccdc_archive' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure _item_description.description ; The mean hydrostatic pressure in kilopascals at which the intensities were measured. ; _item.name '_diffrn.ambient_pressure' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'kilopascals' _item_related.related_name '_diffrn.ambient_pressure_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_pressure' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure_esd _item_description.description ; The estimated standard deviation of _diffrn.ambient_pressure. ; _item.name '_diffrn.ambient_pressure_esd' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_units.code 'kilopascals' _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_diffrn_ambient_pressure' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure_gt _item_description.description ; The mean hydrostatic pressure in kilopascals above which the intensities were measured. _diffrn.ambient_pressure_gt and _diffrn.ambient_pressure_lt allow a pressure range to be given. _diffrn.ambient_pressure should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_pressure_gt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'kilopascals' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_pressure_gt' cif_core.dic 2.3 save_ save__diffrn.ambient_pressure_lt _item_description.description ; The mean hydrostatic pressure in kilopascals below which the intensities were measured. _diffrn.ambient_pressure_gt and _diffrn.ambient_pressure_lt allow a pressure range to be given. _diffrn.ambient_pressure should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_pressure_lt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'kilopascals' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_pressure_lt' cif_core.dic 2.3 save_ # save__diffrn.ambient_temperature # _item_description.description # ; The mean temperature in kelvins at which the intensities # were measured. # ; # _item.name '_diffrn.ambient_temperature' # _item.category_id diffrn # _item.mandatory_code no # _item_type.code float # _item_type_conditions.code esd # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # _item_units.code kelvins # _item_related.related_name '_diffrn.ambient_temperature_esd' # _item_related.function_code associated_esd # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_diffrn_ambient_temperature' cif_core.dic 2.3 # save_ #save__diffrn.ambient_temperature_esd # _item_description.description #; The estimated standard deviation of _diffrn.ambient_temp. #; # _item.name '_diffrn.ambient_temperature_esd' # _item.category_id diffrn # _item.mandatory_code no # _item_type.code float # _item_units.code kelvins # _item_related.related_name '_diffrn.ambient_temp' # _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_diffrn_ambient_temperature_esd' cif_core.dic 2.3 # save_ save__diffrn.ambient_temp_gt _item_description.description ; The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. _diffrn.ambient_temp should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_temp_gt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_temperature_gt' cif_core.dic 2.3 save_ save__diffrn.ambient_temp_lt _item_description.description ; The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. _diffrn.ambient_temp should always be used in preference to these two items whenever possible. ; _item.name '_diffrn.ambient_temp_lt' _item.category_id diffrn _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_ambient_temperature_lt' cif_core.dic 2.3 save_ save__diffrn_attenuator.material _item_description.description ; Material from which the attenuator is made. ; _item.name '_diffrn_attenuator.material' _item.category_id diffrn_attenuator _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_attenuator_material' cif_core.dic 2.3 save_ save__diffrn_detector.area_resol_mean _item_description.description ; The resolution of an area detector, in pixels/mm. ; _item.name '_diffrn_detector.area_resol_mean' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'pixels_per_millimetre' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_detector_area_resol_mean' cif_core.dic 2.3 save_ save__diffrn_detector.dtime _item_description.description ; The deadtime in microseconds of the detector used to measure the diffraction intensities. ; _item.name '_diffrn_detector.dtime' _item.category_id diffrn_detector _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . # _item_related.related_name '_diffrn_radiation_detector.dtime' # _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_detector_dtime' cif_core.dic 2.3 save_ save__diffrn_refln.class_code _item_description.description ; The code identifying the class to which this reflection has been assigned. This code must match a value of _diffrn_reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. ; _item.name '_diffrn_refln.class_code' _item.category_id diffrn_refln _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_refln_class_code' cif_core.dic 2.3 save_ save__diffrn_refln.intensity_u _item_description.description ; Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. ; _item.name '_diffrn_refln.intensity_u' _item.category_id diffrn_refln _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_refln.intensity_sigma' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_refln_intensity_u' cif_core.dic 2.3 save_ save__diffrn_reflns.av_unetI/netI _item_description.description ; Measure [sum u(net I)|/sum|net I|] for all measured reflections. ; _item.name '_diffrn_reflns.av_unetI/netI' _item.category_id diffrn_reflns _item.mandatory_code no _item_type.code float # _item_related.related_name '_diffrn_reflns.av_sigmaI/netI' # _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_av_unetI/netI' cif_core.dic 2.3 save_ ######################### ## DIFFRN_REFLNS_CLASS ## ######################### save_diffrn_reflns_class _category.description ; Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment. ; _category.id 'diffrn_reflns_class' _category.mandatory_code no _category_key.name '_diffrn_reflns_class.code' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _diffrn_reflns_class.number _diffrn_reflns_class.d_res_high _diffrn_reflns_class.d_res_low _diffrn_reflns_class.av_R_eq _diffrn_reflns_class.code _diffrn_reflns_class.description 1580 0.551 6.136 0.015 'Main' 'm=0; main reflections' 1045 0.551 6.136 0.010 'Sat1' 'm=1; first-order satellites' ; ; Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_reflns_class.av_R_eq _item_description.description ; For each reflection class, the residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The av|del(I)| term is the average absolute difference between av(I) and the individual intensities. ; _item.name '_diffrn_reflns_class.av_R_eq' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_av_R_eq' cif_core.dic 2.3 save_ save__diffrn_reflns_class.av_sgI/I _item_description.description ; Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities in a reflection class. ; _item.name '_diffrn_reflns_class.av_sgI/I' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_reflns_class.av_uI/I' _item_related.function_code replaces loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_av_sgI/I' cif_core.dic 2.3 save_ save__diffrn_reflns_class.av_uI/I _item_description.description ; Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. ; _item.name '_diffrn_reflns_class.av_uI/I' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_reflns_class.av_sgI/I' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_av_uI/I' cif_core.dic 2.3 save_ save__diffrn_reflns_class.code _item_description.description ; The code identifying a certain reflection class. ; _item.name '_diffrn_reflns_class.code' _item.category_id diffrn_reflns_class _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' 'm1' 's2' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_code' cif_core.dic 2.3 save_ save__diffrn_reflns_class.description _item_description.description ; Description of each reflection class. ; _item.name '_diffrn_reflns_class.description' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'm=1 first order satellites' 'H0L0 common projection reflections' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_description' cif_core.dic 2.3 save_ save__diffrn_reflns_class.d_res_high _item_description.description ; The smallest value in angstroms for the interplanar spacings for the reflections in each measured reflection class. This is called the highest resolution for this reflection class. ; _item.name '_diffrn_reflns_class.d_res_high' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_d_res_high' cif_core.dic 2.3 save_ save__diffrn_reflns_class.d_res_low _item_description.description ; The largest value in angstroms of the interplanar spacings for the reflections for each measured reflection class. This is called the lowest resolution for this reflection class. ; _item.name '_diffrn_reflns_class.d_res_low' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_d_res_low' cif_core.dic 2.3 save_ save__diffrn_reflns_class.number _item_description.description ; The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations. ; _item.name '_diffrn_reflns_class.number' _item.category_id diffrn_reflns_class _item.mandatory_code no _item_type.code int loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_reflns_class_number' cif_core.dic 2.3 save_ save__diffrn_source.take-off_angle _item_description.description ; The complement of the angle in degrees between the normal to the surface of the X-ray tube target and the primary X-ray beam for beams generated by traditional X-ray tubes. ; _item.name '_diffrn_source.take-off_angle' _item.category_id diffrn_source _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.00 0.00 0.00 90.0 90.0 90.0 _item_examples.case 1.5 _item_units.code 'degrees' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_source_take-off_angle' cif_core.dic 2.3 save_ save__diffrn_standards.scale_u _item_description.description ; The standard uncertainty of the individual mean standard scales applied to the intensity data. ; _item.name '_diffrn_standards.scale_u' _item.category_id diffrn_standards _item.mandatory_code no _item_type.code float _item_related.related_name '_diffrn_standards.scale_sigma' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_standards_scale_u' cif_core.dic 2.3 save_ save__exptl_crystal.colour_lustre _item_description.description ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'. ; _item.name '_exptl_crystal.colour_lustre' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value metallic dull clear _item_related.related_name '_exptl_crystal.colour' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_colour_lustre' cif_core.dic 2.3 save_ save__exptl_crystal.colour_modifier _item_description.description ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'. ; _item.name '_exptl_crystal.colour_modifier' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value light dark whitish blackish grayish brownish reddish pinkish orangish yellowish greenish bluish _item_related.related_name '_exptl_crystal.colour' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_colour_modifier' cif_core.dic 2.3 save_ save__exptl_crystal.colour_primary _item_description.description ; The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'. ; _item.name '_exptl_crystal.colour_primary' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code line loop_ _item_enumeration.value colourless white black gray brown red pink orange yellow green blue violet _item_related.related_name '_exptl_crystal.colour' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_colour_primary' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas _item_description.description ; Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). ; _item.name '_exptl_crystal.density_meas' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas_esd' _item_related.function_code associated_esd loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_esd _item_description.description ; The estimated standard deviation of _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_meas_esd' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas' _item_related.function_code associated_value # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_exptl_crystal_density_meas_esd' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_gt _item_description.description ; The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which _exptl_crystal.density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_meas_gt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 2.5 ; lower limit for the density (only the range within which the density lies was given in the original paper) ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_gt' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_lt _item_description.description ; The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which _exptl_crystal.density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal.density_meas. ; _item.name '_exptl_crystal.density_meas_lt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'megagrams_per_cubic_metre' _item_related.related_name '_exptl_crystal.density_meas' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 1.0 'specimen floats in water' 5.0 ; upper limit for the density (only the range within which the density lies was given in the original paper) ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_lt' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp _item_description.description ; Temperature in kelvins at which _exptl_crystal.density_meas was determined. ; _item.name '_exptl_crystal.density_meas_temp' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_type_conditions.code esd loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_temp' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp_esd _item_description.description ; The estimated standard deviation of _exptl_crystal.density_meas_temp. ; _item.name '_exptl_crystal.density_meas_temp_esd' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float _item_units.code kelvins # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_exptl_crystal_density_meas_temp_esd' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp_gt _item_description.description ; Temperature in kelvins above which _exptl_crystal.density_meas was determined. _exptl_crystal.density_meas_temp_gt and _exptl_crystal.density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal.density_meas_temp. ; _item.name '_exptl_crystal.density_meas_temp_gt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_exptl_crystal.density_meas_temp' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_temp_gt' cif_core.dic 2.3 save_ save__exptl_crystal.density_meas_temp_lt _item_description.description ; Temperature in kelvins below which _exptl_crystal.density_meas was determined. _exptl_crystal.density_meas_temp_gt and _exptl_crystal.density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal.density_meas_temp. ; _item.name '_exptl_crystal.density_meas_temp_lt' _item.category_id exptl_crystal _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code kelvins _item_related.related_name '_exptl_crystal.density_meas_temp' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 300 ; The density was measured at some unspecified temperature below room temperature. ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_exptl_crystal_density_meas_temp_lt' cif_core.dic 2.3 save_ save__geom_bond.valence _item_description.description ; The bond valence calculated from _geom_bond.dist. ; _item.name '_geom_bond.valence' _item.category_id geom_bond _item.mandatory_code no _item_type.code int loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_geom_bond_valence' cif_core.dic 2.3 save_ save__publ_author.id_iucr _item_description.description ; Identifier in the IUCr contact database of a publication author. This identifier may be available from the World Directory of Crystallographers (http://wdc.iucr.org). ; _item.name '_publ_author.id_iucr' _item.category_id publ_author _item.mandatory_code no _item_type.code code _item_examples.case 2985 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_publ_author_id_iucr' cif_core.dic 2.3 save_ save__refine.ls_R_factor_gt _item_description.description ; Residual factor for the reflections (with number given by _reflns.number_gt) judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. This is the conventional R factor. See also _refine.ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections ; _item.name '_refine.ls_R_factor_gt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_R_factor_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_R_factor_gt' cif_core.dic 2.3 save_ save__refine.ls_goodness_of_fit_gt _item_description.description ; The least-squares goodness-of-fit parameter S for significantly intense reflections (see _reflns.threshold_expression) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine.ls_restrained_S_ definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_gt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_goodness_of_fit_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_goodness_of_fit_gt' cif_core.dic 2.3 save_ save__refine.ls_goodness_of_fit_ref _item_description.description ; The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections ; _item.name '_refine.ls_goodness_of_fit_ref' _item.category_id refine _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_goodness_of_fit_ref' cif_core.dic 2.3 save_ # save__refine.ls_shift/esd_max # _item_description.description # ; The largest ratio of the final least-squares parameter # shift to the final standard uncertainty (s.u., # formerly described as estimated standard deviation, e.s.d.). # ; # _item.name '_refine.ls_shift/esd_max' # _item.category_id refine # _item.mandatory_code no # _item_type.code float # _item_related.related_name '_refine.ls_shift/su_max' # _item_related.function_code replaces # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refine_ls_shift/esd_max' cif_core.dic 2.3 # save_ # # save__refine.ls_shift/esd_mean # _item_description.description # ; The average ratio of the final least-squares parameter # shift to the final standard uncertainty (s.u., # formerly described as estimated standard deviation, e.s.d.). # ; # # _item.name '_refine.ls_shift/esd_mean' # _item.category_id refine # _item.mandatory_code no # _item_type.code float # _item_related.related_name '_refine.ls_shift/su_mean' # _item_related.function_code replaces # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refine_ls_shift/esd_mean' cif_core.dic 2.3 # save_ save__refine.ls_shift_over_su_max _item_description.description ; The largest ratio of the final least-squares parameter shift to the final standard uncertainty. ; _item.name '_refine.ls_shift_over_su_max' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_esd_max' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_max' cif_core.dic 2.3 save_ save__refine.ls_shift_over_su_max_lt _item_description.description ; An upper limit for the largest ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the largest value of the shift divided by the final standard uncertainty is too small to measure. ; _item.name '_refine.ls_shift_over_su_max_lt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_su_max' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_max_lt' cif_core.dic 2.3 save_ save__refine.ls_shift_over_su_mean _item_description.description ; The average ratio of the final least-squares parameter shift to the final standard uncertainty. ; _item.name '_refine.ls_shift_over_su_mean' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_esd_mean' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_mean' cif_core.dic 2.3 save_ save__refine.ls_shift_over_su_mean_lt _item_description.description ; An upper limit for the average ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the average value of the shift divided by the final standard uncertainty is too small to measure. ; _item.name '_refine.ls_shift_over_su_mean_lt' _item.category_id refine _item.mandatory_code no _item_type.code float _item_related.related_name '_refine.ls_shift_over_su_mean' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_shift/su_mean_lt' cif_core.dic 2.3 save_ ##################### ## REFINE_LS_CLASS ## ##################### save_refine_ls_class _category.description ; Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately. ; _category.id 'refine_ls_class' _category.mandatory_code no _category_key.name '_refine_ls_class.code' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _refine_ls_class.R_factor_gt _refine_ls_class.code 0.057 'Main' 0.074 'Com' 0.064 'NbRefls' 0.046 'LaRefls' 0.112 'Sat1' 0.177 'Sat2' ; ; Example 1 - data for a modulated structure from van Smaalen [J. Phys. Condens. Matter (1991), 3, 1247-1263]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__refine_ls_class.code _item_description.description ; The code identifying a certain reflection class. This code must match a _reflns_class.code. ; _item.name '_refine_ls_class.code' _item.category_id refine_ls_class _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' 'm1' 's2' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_code' cif_core.dic 2.3 save_ save__refine_ls_class.d_res_high _item_description.description ; For each reflection class, the lowest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. ; _item.name '_refine_ls_class.d_res_high' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_d_res_high' cif_core.dic 2.3 save_ save__refine_ls_class.d_res_low _item_description.description ; For each reflection class, the highest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. ; _item.name '_refine_ls_class.d_res_low' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_d_res_low' cif_core.dic 2.3 save_ save__refine_ls_class.R_factor_gt _item_description.description ; For each reflection class, the residual factor for significantly intense reflections (see _reflns.threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of _refine_ls_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_factor_gt' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_factor_gt' cif_core.dic 2.3 save_ save__refine_ls_class.R_factor_all _item_description.description ; For each reflection class, the residual factor for all reflections satisfying the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of _refine_ls_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_factor_all' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_factor_all' cif_core.dic 2.3 save_ save__refine_ls_class.R_Fsqd_factor _item_description.description ; For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors, for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_Fsqd_factor' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_Fsqd_factor' cif_core.dic 2.3 save_ save__refine_ls_class.R_I_factor _item_description.description ; For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~ sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.R_I_factor' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_R_I_factor' cif_core.dic 2.3 save_ save__refine_ls_class.wR_factor_all _item_description.description ; For each reflection class, the weighted residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. See also the _refine_ls_class.R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine.ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight and the sum is taken over the reflections of this class. ; _item.name '_refine_ls_class.wR_factor_all' _item.category_id refine_ls_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refine_ls_class_wR_factor_all' cif_core.dic 2.3 save_ save__refln.class_code _item_description.description ; The code identifying the class to which this reflection has been assigned. This code must match a value of _reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. ; _item.name '_refln.class_code' _item.category_id refln _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_class_code' cif_core.dic 2.3 save_ save__refln.d_spacing _item_description.description ; The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression _refln.d_spacing = 2/(_refln.sint/lambda). ; _item.name '_refln.d_spacing' _item.category_id refln _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_d_spacing' cif_core.dic 2.3 save_ save__refln.include_status _item_description.description ; Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. ; _item.name '_refln.include_status' _item.category_id refln _item.mandatory_code no _item_type.code code _item_related.related_name '_refln.status' _item_related.function_code alternate loop_ _item_enumeration.value _item_enumeration.detail o ; (lower-case letter o for 'observed') satisfies _refine.ls_d_res_high satisfies _refine.ls_d_res_low exceeds _reflns.threshold_expression ; < ; satisfies _refine.ls_d_res_high satisfies _refine.ls_d_res_low does not exceed _reflns.threshold_expression ; - 'systematically absent reflection' x 'unreliable measurement -- not used' h 'does not satisfy _refine.ls_d_res_high' l 'does not satisfy _refine.ls_d_res_low' # _item_default.value o loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_include_status' cif_core.dic 2.3 save_ save__refln.mean_path_length_tbar _item_description.description ; Mean path length in millimetres through the crystal for this reflection. ; _item.name '_refln.mean_path_length_tbar' _item.category_id refln _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'millimetres' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_refln_mean_path_length_tbar' cif_core.dic 2.3 save_ # save__refln.observed_status # _item_description.description # ; Classification of a reflection so as to indicate its status # with respect to inclusion in refinement and calculation of # R factors. # ; # # _item.name '_refln.observed_status' # _item.category_id refln # _item.mandatory_code no # _item_type.code code # _item_related.related_name '_refln.include_status' # _item_related.function_code replaces # loop_ # _item_enumeration.value # _item_enumeration.detail # o # ; satisfies _refine.ls_d_res_high # satisfies _refine.ls_d_res_low # observed by _reflns_observed_criterion # ; # < # ; satisfies _refine.ls_d_res_high # satisfies _refine.ls_d_res_low # unobserved by _reflns.observed_criterion # ; # - 'systematically absent reflection' # x 'unreliable measurement -- not used' # h 'does not satisfy _refine.ls_d_res_high' # l 'does not satisfy _refine.ls_d_res_low' # # # _item_default.value o # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refln_observed_status' cif_core.dic 2.3 # save_ # save__refln.sint/lambda # _item_description.description # ; The (sin theta)/lambda value in reciprocal angstroms for this # reflection. # ; # _item.name '_refln.sint/lambda' # _item.category_id refln # _item.mandatory_code no # _item_type.code float # loop_ # _item_range.minimum # _item_range.maximum # 0.0 0.0 # 0.0 . # _item_units.code 'reciprocal_angstroms' # loop_ # _item_aliases.alias_name # _item_aliases.dictionary # _item_aliases.version # '_refln_sint/lambda' cif_core.dic 2.3 # save_ save__reflns.Friedel_coverage _item_description.description ; The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item _reflns.number_all. This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, the value of _reflns.Friedel_coverage is necessarily equal to 0.0, as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, _reflns.Friedel_coverage is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, _reflns.Friedel_coverage will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in space group Pmm2, measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for _reflns.Friedel_coverage. ; _item.name '_reflns.Friedel_coverage' _item.category_id reflns _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 1.0 1.0 1.0 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_Friedel_coverage' cif_core.dic 2.3 save_ save__reflns.number_gt _item_description.description ; The number of reflections in the REFLN list (not the DIFFRN_REFLN list) that are significantly intense, satisfying the criterion specified by _reflns.threshold_expression. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details. ; _item.name '_reflns.number_gt' _item.category_id reflns _item.mandatory_code no _item_type.code int # _item_related.related_name '_reflns.number_observed' # _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_number_gt' cif_core.dic 2.3 save_ save__reflns.threshold_expression _item_description.description ; The threshold, usually based on multiples of u(I), u(F^2^) or u(F), that serves to identify significantly intense reflections, the number of which is given by _reflns.number_gt. These reflections are used in the calculation of _refine.ls_R_factor_gt. ; _item.name '_reflns.threshold_expression' _item.category_id reflns _item.mandatory_code no _item_aliases.alias_name '_reflns_threshold_expression' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.3 loop_ _item_related.related_name _item_related.function_code '_reflns.observed_criterion' alternate _item_type.code text _item_examples.case 'I>2u(I)' save_ ################## ## REFLNS_CLASS ## ################## save_reflns_class _category.description ; Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class. ; _category.id 'reflns_class' _category.mandatory_code no _category_key.name '_reflns_class.code' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _reflns_class.number_gt _reflns_class.code 584 'Main' 226 'Sat1' 50 'Sat2' ; ; Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__reflns_class.code _item_description.description ; The code identifying a certain reflection class. ; _item.name '_reflns_class.code' _item.category_id reflns_class _item.mandatory_code yes _item_type.code code loop_ _item_examples.case '1' 'm1' 's2' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_code' cif_core.dic 2.3 save_ save__reflns_class.description _item_description.description ; Description of each reflection class. ; _item.name '_reflns_class.description' _item.category_id reflns_class _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'm=1 first order satellites' 'H0L0 common projection reflections' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_description' cif_core.dic 2.3 save_ save__reflns_class.d_res_high _item_description.description ; For each reflection class, the smallest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. ; _item.name '_reflns_class.d_res_high' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_d_res_high' cif_core.dic 2.3 save_ save__reflns_class.d_res_low _item_description.description ; For each reflection class, the largest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. ; _item.name '_reflns_class.d_res_low' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_d_res_low' cif_core.dic 2.3 save_ save__reflns_class.number_gt _item_description.description ; For each reflection class, the number of significantly intense reflections (see _reflns.threshold_expression) in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel- equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details. ; _item.name '_reflns_class.number_gt' _item.category_id reflns_class _item.mandatory_code no _item_type.code int loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_number_gt' cif_core.dic 2.3 save_ save__reflns_class.number_total _item_description.description ; For each reflection class, the total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details. ; _item.name '_reflns_class.number_total' _item.category_id reflns_class _item.mandatory_code no _item_type.code int loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_number_total' cif_core.dic 2.3 save_ save__reflns_class.R_factor_all _item_description.description ; For each reflection class, the residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of _reflns_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_factor_all' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_factor_all' cif_core.dic 2.3 save_ save__reflns_class.R_factor_gt _item_description.description ; For each reflection class, the residual factor for significantly intense reflections (see _reflns.threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of _reflns_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_factor_gt' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_factor_gt' cif_core.dic 2.3 save_ save__reflns_class.R_Fsqd_factor _item_description.description ; For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_Fsqd_factor' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_Fsqd_factor' cif_core.dic 2.3 save_ save__reflns_class.R_I_factor _item_description.description ; For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.R_I_factor' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_R_I_factor' cif_core.dic 2.3 save_ save__reflns_class.wR_factor_all _item_description.description ; For each reflection class, the weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. See also _reflns_class.R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by _refine.ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight and the sum is taken over the reflections of this class. ; _item.name '_reflns_class.wR_factor_all' _item.category_id reflns_class _item.mandatory_code no _item_type.code float loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_class_wR_factor_all' cif_core.dic 2.3 save_ save__reflns_shell.meanI_over_sigI_gt _item_description.description ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. ; _item.name '_reflns_shell.meanI_over_sigI_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.meanI_over_uI_gt' _item_related.function_code replaces loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_meanI_over_sigI_gt' cif_core.dic 2.3 save_ save__reflns_shell.meanI_over_uI_all _item_description.description ; The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. ; _item.name '_reflns_shell.meanI_over_uI_all' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.meanI_over_sigI_all' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_meanI_over_uI_all' cif_core.dic 2.3 save_ save__reflns_shell.meanI_over_uI_gt _item_description.description ; The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. ; _item.name '_reflns_shell.meanI_over_uI_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float loop_ _item_related.related_name _item_related.function_code '_reflns_shell.meanI_over_sigI_gt' alternate '_reflns_shell.meanI_over_sigI_obs' alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_meanI_over_uI_gt' cif_core.dic 2.3 save_ save__reflns_shell.number_measured_gt _item_description.description ; The number of significantly intense reflections (see _reflns.threshold_expression) measured for this shell. ; _item.name '_reflns_shell.number_measured_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code int _item_related.related_name '_reflns_shell.number_measured_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_number_measured_gt' cif_core.dic 2.3 save_ save__reflns_shell.number_unique_gt _item_description.description ; The total number of significantly intense reflections (see _reflns.threshold_expression) resulting from merging measured symmetry-equivalent reflections for this resolution shell. ; _item.name '_reflns_shell.number_unique_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code int _item_related.related_name '_reflns_shell.number_unique_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0 0 0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_number_unique_gt' cif_core.dic 2.3 save_ save__reflns_shell.percent_possible_gt _item_description.description ; The percentage of geometrically possible reflections represented by significantly intense reflections (see _reflns.threshold_expression) measured for this shell. ; _item.name '_reflns_shell.percent_possible_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.percent_possible_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 100.0 100.0 100.0 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_percent_possible_gt' cif_core.dic 2.3 save_ save__reflns_shell.Rmerge_F_gt _item_description.description ; The value of Rmerge(F) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sum~i~ ( sum~j~ | F~j~ - | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ ) F~j~ = the amplitude of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. ; _item.name '_reflns_shell.Rmerge_F_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.Rmerge_F_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_Rmerge_F_gt' cif_core.dic 2.3 save_ save__reflns_shell.Rmerge_I_gt _item_description.description ; The value of Rmerge(I) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sum~i~ ( sum~j~ | I~j~ - | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ ) I~j~ = the intensity of the jth observation of reflection i = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. ; _item.name '_reflns_shell.Rmerge_I_gt' _item.category_id reflns_shell _item.mandatory_code no _item_type.code float _item_related.related_name '_reflns_shell.Rmerge_I_obs' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 0.0 0.0 0.0 . loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_reflns_shell_Rmerge_I_gt' cif_core.dic 2.3 save_ ################# ## SPACE_GROUP ## ################# save_space_group _category.description ; Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary. ; _category.id 'space_group' _category.mandatory_code no _category_key.name '_space_group.id' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _space_group.id 1 _space_group.name_H-M_alt 'C 2/c' _space_group.IT_number 15 _space_group.name_Hall '-C 2yc' _space_group.crystal_system monoclinic ; ; Example 1 - the monoclinic space group No. 15 with unique axis b. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__space_group.crystal_system _item_description.description ; The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs. Note that rhombohedral space groups belong to the trigonal system. ; _item.name '_space_group.crystal_system' _item.category_id space_group _item.mandatory_code no _item_type.code code _item_related.related_name '_symmetry.cell_setting' _item_related.function_code alternate loop_ _item_enumeration.value triclinic monoclinic orthorhombic tetragonal trigonal hexagonal cubic loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_crystal_system' cif_core.dic 2.3 save_ save__space_group.id _item_description.description ; This is the unique identifier for the SPACE_GROUP category. ; _item.name '_space_group.id' _item.category_id space_group _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_id' cif_core.dic 2.3 save_ save__space_group.IT_number _item_description.description ; The number as assigned in International Tables for Crystallography Vol. A, specifying the proper affine class (i.e. the orientation-preserving affine class) of space groups (crystallographic space-group type) to which the space group belongs. This number defines the space-group type but not the coordinate system in which it is expressed. ; _item.name '_space_group.IT_number' _item.category_id space_group _item.mandatory_code no _item_type.code int _item_related.related_name '_symmetry.Int_Tables_number' _item_related.function_code alternate loop_ _item_range.minimum _item_range.maximum 1 1 1 230 230 230 loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_IT_number' cif_core.dic 2.3 save_ save__space_group.name_Hall _item_description.description ; Space-group symbol defined by Hall. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. _space_group.name_Hall uniquely defines the space group and its reference to a particular coordinate system. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. [See also International Tables for Crystallography Vol. B (2001), Chapter 1.4, Appendix 1.4.2.] ; _item.name '_space_group.name_Hall' _item.category_id space_group _item.mandatory_code no _item_type.code line _item_related.related_name '_symmetry.space_group_name_Hall' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 'P 2c -2ac' 'equivalent to Pca21' '-I 4bd 2ab 3' 'equivalent to Ia3d' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_name_Hall' cif_core.dic 2.3 save_ save__space_group.name_H-M_alt _item_description.description ; _space_group.name_H-M_alt allows any Hermann-Mauguin symbol to be given. The way in which this item is used is determined by the user and in general is not intended to be interpreted by computer. It may, for example, be used to give one of the extended Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. Subscripts should appear without special symbols. Bars should be given as negative signs before the numbers to which they apply. The commonly used Hermann-Mauguin symbol determines the space- group type uniquely but a given space-group type may be described by more than one Hermann-Mauguin symbol. The space- group type is best described using _space_group.IT_number. The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use _space_group.name_Hall or list the symmetry operations. ; _item.name '_space_group.name_H-M_alt' _item.category_id space_group _item.mandatory_code no _item_type.code line _item_related.related_name '_symmetry.space_group_name_H-M' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail ; loop_ _space_group.name_H-M_alt 'C m c m' 'C 2/c 2/m 21/m' 'A m a m' ; 'three examples for space group No. 63' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_name_H-M_alt' cif_core.dic 2.3 save_ ####################### ## SPACE_GROUP_SYMOP ## ####################### save_space_group_symop _category.description ; Contains information about the symmetry operations of the space group. ; _category.id 'space_group_symop' _category.mandatory_code no _category_key.name '_space_group_symop.id' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,-y,-z 3 -x,1/2+y,1/2-z 4 x,1/2-y,1/2+z ; ; Example 1 - The symmetry operations for the space group P21/c. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__space_group_symop.id _item_description.description ; An arbitrary identifier that uniquely labels each symmetry operation in the list. ; _item.name '_space_group_symop.id' _item.category_id space_group_symop _item.mandatory_code yes _item_type.code code _item_related.related_name '_symmetry_equiv.id' _item_related.function_code alternate loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_symop_id' cif_core.dic 2.3 save_ save__space_group_symop.operation_xyz _item_description.description ; A parsable string giving one of the symmetry operations of the space group in algebraic form. If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by the fractions, an equivalent position X' is generated from a given position X by the equation X' = WX + w (Note: X is used to represent bold_italics_x in International Tables for Crystallography Vol. A, Part 5) When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicity all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used. ; _item.name '_space_group_symop.operation_xyz' _item.category_id space_group_symop _item.mandatory_code no _item_type.code line # _item_default.value 'x,y,z' _item_related.related_name '_symmetry_equiv.pos_as_xyz' _item_related.function_code alternate loop_ _item_examples.case _item_examples.detail 'x,1/2-y,1/2+z' ; glide reflection through the plane (x,1/4,z), with glide vector 1/2 c ; loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_symop_operation_xyz' cif_core.dic 2.3 save_ save__space_group_symop.sg_id _item_description.description ; This must match a particular value of _space_group.id, allowing the symmetry operation to be identified with a particular space group. ; _item.name '_space_group_symop.sg_id' _item.category_id space_group_symop _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_space_group_symop_sg_id' cif_core.dic 2.3 save_ ################### ## VALENCE_PARAM ## ################### save_valence_param _category.description ; Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken. ; _category.id 'valence_param' _category.mandatory_code no loop_ _category_key.name '_valence_param.atom_1' '_valence_param.atom_1_valence' '_valence_param.atom_2' '_valence_param.atom_2_valence' loop_ _category_examples.case _category_examples.detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _valence_param.atom_1 _valence_param.atom_1_valence _valence_param.atom_2 _valence_param.atom_2_valence _valence_param.Ro _valence_param.B _valence_param.ref_id _valence_param.details Cu 2 O -2 1.679 0.37 a . Cu 2 O -2 1.649 0.37 j . Cu 2 N -3 1.64 0.37 m '2-coordinate N' Cu 2 N -3 1.76 0.37 m '3-coordinate N' loop_ _valence_ref.id _valence_ref.reference a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247' j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205' m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375' ; ; Example 1 - a bond-valence parameter list with accompanying references. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__valence_param.atom_1 _item_description.description ; The element symbol of the first atom forming the bond whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_1' _item.category_id valence_param _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_1' cif_core.dic 2.3 save_ save__valence_param.atom_1_valence _item_description.description ; The valence (formal charge) of the first atom whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_1_valence' _item.category_id valence_param _item.mandatory_code yes _item_type.code int loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_1_valence' cif_core.dic 2.3 save_ save__valence_param.atom_2 _item_description.description ; The element symbol of the second atom forming the bond whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_2' _item.category_id valence_param _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_2' cif_core.dic 2.3 save_ save__valence_param.atom_2_valence _item_description.description ; The valence (formal charge) of the second atom whose bond-valence parameters are given in this category. ; _item.name '_valence_param.atom_2_valence' _item.category_id valence_param _item.mandatory_code yes _item_type.code int loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_atom_2_valence' cif_core.dic 2.3 save_ save__valence_param.B _item_description.description ; The bond-valence parameter B used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. ; _item.name '_valence_param.B' _item.category_id valence_param _item.mandatory_code no _item_type.code float _item_units.code 'angstroms' loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_B' cif_core.dic 2.3 save_ save__valence_param.details _item_description.description ; Details of or comments on the bond-valence parameters. ; _item.name '_valence_param.details' _item.category_id valence_param _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_details' cif_core.dic 2.3 save_ save__valence_param.id _item_description.description ; An identifier for the valence parameters of a bond between the given atoms. ; _item.name '_valence_param.id' _item.category_id valence_param _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_id' cif_core.dic 2.3 save_ save__valence_param.ref_id _item_description.description ; An identifier which links to the reference to the source from which the bond-valence parameters are taken. A child of _valence_ref.id which it must match. ; _item.name '_valence_param.ref_id' _item.category_id valence_param _item.mandatory_code no _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_ref_id' cif_core.dic 2.3 save_ save__valence_param.Ro _item_description.description ; The bond-valence parameter Ro used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. ; _item.name '_valence_param.Ro' _item.category_id valence_param _item.mandatory_code no _item_type.code float _item_units.code angstroms loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_param_Ro' cif_core.dic 2.3 save_ ################# ## VALENCE_REF ## ################# save_valence_ref _category.description ; Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken. ; _category.id 'valence_ref' _category.mandatory_code no _category_key.name '_valence_ref.id' save_ save__valence_ref.id _item_description.description ; An identifier for items in this category. Parent of _valence_param.ref_id, which must have the same value. ; _item.name '_valence_ref.id' _item.category_id valence_ref _item.mandatory_code yes _item_type.code code loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_ref_id' cif_core.dic 2.3 save_ save__valence_ref.reference _item_description.description ; Literature reference from which the valence parameters identified by _valence_param.id were taken. ; _item.name '_valence_ref.reference' _item.category_id valence_ref _item.mandatory_code no _item_type.code text loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_valence_ref_reference' cif_core.dic 2.3 save_ #-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof