############################################################################## # # # CIF PRIVATE IUCR DEFINITIONS # # ---------------------------- # # # # This dictionary contains the names and definitions of "private" data items # # recognised by the International Union of Crystallography for internal # # processing of CIFs submitted for publication in IUCr journals. # # # # Items prefixed with the registered string _publcif_ are intended to be # # created and maintained automatically by the application publCIF # # # # Copyright 2014 International Union of Crystallography # ############################################################################## data_on_this_dictionary _dictionary_name cif_iucr.dic _dictionary_version 1.2 _dictionary_update 2014-07-09 _dictionary_history ; 2014-07-09 Added new publCIF items to cater for new journal article formats (SPW/BMcM): _publcif_datablock.id _publcif_datablock_[] _publcif_info_cif.paper_type _publcif_info_cif_[] _publcif_info_exptl_table_use_headnotes _publcif_info_tables.block_id _publcif_info_tables.reference_item _publcif_info_tables_[] 2011-07-04 Added _iucr_refine_instructions_details_constraints _iucr_refine_instructions_details_restraints BMcM 2011-07-04 Added _iucr_refine_instruction_details to accommodate erroneous instructions in published Notes for Authors BMcM 2011-06-24 Additional local items (including some reserved for use by publcif) that have been introduced to accommodate specific aspects of journal production in the IUCr office: _iucr_refine_instructions_details _iucr_geom_hbonds_details _publcif_info_datablock.* _publcif_info_exptl_table_extra_item _publcif_info_exptl_table_header_item _publcif_info_exptl_table_max_cols _publcif_jmolscript.* _iucr_publ_object.* Note that some new data names include a dot character, borrowing from the practice of DDL2-compliant dictionaries. This dictionary, however, remains DDL1 compliant. BMcM 2003-11-17 First version formalises data items used internally for Acta C and Acta E since CIF publication began. This is really an object lesson in how *not* to build private data names, but most of the datanames go back to the very early days of CIF when even things like same-category looped lists were not set in stone. BMcM ; ########### ## AUDIT ## ########### data_iucr_compatibility_tag _name '_iucr_compatibility_tag' _category audit _type char loop_ _enumeration _enumeration_detail ACTA95 'Modify typesetting of R factors etc' _definition ; A code used by IUCr typesetting software to select different printing formats. ; ########## ## GEOM ## ########## data_iucr_geom_hbonds_details _name '_iucr_geom_hbonds_details' _category geom _type char _definition ; Free-text description of any extra details about hydrogen bonds, e.g. explanation of site label when the site does not represent a single element. Will be included as a headnote in a table of hydrogen-bond geometry. ; ###################### ## GEOM_EXTRA_TABLE ## ###################### data_geom_extra_table_[] _name '_geom_extra_table_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _geom_extra_table_head_B ; Geometric parameters (\%A, \%) for C---H..\p interactions in (I) and (II) ; loop_ _geom_extra_tableB_col_1 _geom_extra_tableB_col_2 _geom_extra_tableB_col_3 _geom_extra_tableB_col_4 _geom_extra_tableB_col_5 _geom_extra_tableB_col_6 _geom_extra_tableB_col_7 ? Cpd C---H H..Cg H~perp~^a^ X-H..Cg X..Cg C10-H10..Cg1^i^ I 0.95 3.32 2.97 140 4.096 ? II 0.95 3.41 2.91 137 4.149 C12-H12..Cg2^ii^ I 0.95 3.17 2.79 171 4.115 ? II 0.95 3.24 2.79 166 4.121 _geom_table_footnote_B ; Note: (a) H~perp~ is the perpendicular distance of the H atom from the plane of the benzene ring. Symmetry codes (i) 1-x, 1/2+y, 1-z; (ii) 1-x, y-1/2, -z. ; ; ; Example 1 - based on data set I of Bomfim, Filgueiras, Howie, Skakle & Wardell, [(2003). Acta Cryst. C59, m526-m529]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; GEOM_EXTRA_TABLE and GEOM_EXTRA_TABLES are private categories of the IUCr used to store arbitrary geometric parameters in a regular format suitable for the automatic generation of printed tables, but without defining specifically the quantities thus tabulated. They are therefore not suitable for the standard interchange of specific machine-interpretable data, and should only be used if there are no suitable formal definitions in the CIF dictionary. ; data_geom_extra_tableA_col_ loop_ _name '_geom_extra_tableA_col_1' '_geom_extra_tableA_col_2' '_geom_extra_tableA_col_3' '_geom_extra_tableA_col_4' '_geom_extra_tableA_col_5' '_geom_extra_tableA_col_6' '_geom_extra_tableA_col_7' '_geom_extra_tableA_col_8' '_geom_extra_tableA_col_9' '_geom_extra_tableA_col_10' '_geom_extra_tableA_col_11' '_geom_extra_tableA_col_12' '_geom_extra_tableA_col_13' '_geom_extra_tableA_col_14' _category geom_extra_table _type char _definition ; Arbitrary geometric data tabulated for print publication. These should not be used in the tabulation of standard geometric properties (use instead the categories GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND, GEOM_TORSION), but may be useful for creating and annotating printed tables. Because of the arbitrariness of the description, these values are not recoverable by general parsers. The table may be implicitly associated with heading, head note and footnote by using the data items in the GEOM_EXTRA_TABLES category labelled with the code A. ; data_geom_extra_tableB_col_ loop_ _name '_geom_extra_tableB_col_1' '_geom_extra_tableB_col_2' '_geom_extra_tableB_col_3' '_geom_extra_tableB_col_4' '_geom_extra_tableB_col_5' '_geom_extra_tableB_col_6' '_geom_extra_tableB_col_7' '_geom_extra_tableB_col_8' '_geom_extra_tableB_col_9' '_geom_extra_tableB_col_10' '_geom_extra_tableB_col_11' '_geom_extra_tableB_col_12' '_geom_extra_tableB_col_13' '_geom_extra_tableB_col_14' _category geom_extra_table _type char _definition ; Arbitrary geometric data tabulated for print publication. These should not be used in the tabulation of standard geometric properties (use instead the categories GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND, GEOM_TORSION), but may be useful for creating and annotating printed tables. Because of the arbitrariness of the description, these values are not recoverable by general parsers. The table may be implicitly associated with heading, head note and footnote by using the data items in the GEOM_EXTRA_TABLES category labelled with the code A. ; data_geom_extra_tableC_col_ loop_ _name '_geom_extra_tableC_col_1' '_geom_extra_tableC_col_2' '_geom_extra_tableC_col_3' '_geom_extra_tableC_col_4' '_geom_extra_tableC_col_5' '_geom_extra_tableC_col_6' '_geom_extra_tableC_col_7' '_geom_extra_tableC_col_8' '_geom_extra_tableC_col_9' '_geom_extra_tableC_col_10' '_geom_extra_tableC_col_11' '_geom_extra_tableC_col_12' '_geom_extra_tableC_col_13' '_geom_extra_tableC_col_14' _category geom_extra_table _type char _definition ; Arbitrary geometric data tabulated for print publication. These should not be used in the tabulation of standard geometric properties (use instead the categories GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND, GEOM_TORSION), but may be useful for creating and annotating printed tables. Because of the arbitrariness of the description, these values are not recoverable by general parsers. The table may be implicitly associated with heading, head note and footnote by using the data items in the GEOM_EXTRA_TABLES category labelled with the code C. ; ####################### ## GEOM_EXTRA_TABLES ## ####################### data_geom_extra_tables_[] _name '_geom_extra_tables_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _geom_extra_table_head_B ; Geometric parameters (\%A, \%) for C---H..\p interactions in (I) and (II) ; loop_ _geom_extra_tableB_col_1 _geom_extra_tableB_col_2 _geom_extra_tableB_col_3 _geom_extra_tableB_col_4 _geom_extra_tableB_col_5 _geom_extra_tableB_col_6 _geom_extra_tableB_col_7 ? Cpd C---H H..Cg H~perp~^a^ X-H..Cg X..Cg C10-H10..Cg1^i^ I 0.95 3.32 2.97 140 4.096 ? II 0.95 3.41 2.91 137 4.149 C12-H12..Cg2^ii^ I 0.95 3.17 2.79 171 4.115 ? II 0.95 3.24 2.79 166 4.121 _geom_table_footnote_B ; Note: (a) H~perp~ is the perpendicular distance of the H atom from the plane of the benzene ring. Symmetry codes (i) 1-x, 1/2+y, 1-z; (ii) 1-x, y-1/2, -z. ; ; ; Example 1 - based on data set I of Bomfim, Filgueiras, Howie, Skakle & Wardell, [(2003). Acta Cryst. C59, m526-m529]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; GEOM_EXTRA_TABLE and GEOM_EXTRA_TABLES are private categories of the IUCr used to store arbitrary geometric parameters in a regular format suitable for the automatic generation of printed tables, but without defining specifically the quantities thus tabulated. They are therefore not suitable for the standard interchange of specific machine-interpretable data, and should only be used if there are no suitable formal definitions in the CIF dictionary. ; data_geom_table_footnote_ loop_ _name '_geom_table_footnote_A' '_geom_table_footnote_B' '_geom_table_footnote_C' _category geom_extra_tables _type char _definition ; Footnote for a printed table of arbitrary geometric quantities. This should not be used in the tabulation of standard geometric properties (use instead the categories GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND, GEOM_TORSION), but is a useful device for creating and annotating printed tables. The label A, B or C is implicitly associated with a list of geometric values in the GEOM_EXTRA_TABLE category labelled with a matching value of A, B or C. ; data_geom_extra_table_head_ loop_ _name '_geom_extra_table_head_A' '_geom_extra_table_head_B' '_geom_extra_table_head_C' _category geom_extra_tables _type char _definition ; Heading for a printed table of arbitrary geometric quantities. This should not be used in the tabulation of standard geometric properties (use instead the categories GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND, GEOM_TORSION), but is a useful device for creating and annotating printed tables. The label A, B or C is implicitly associated with a list of geometric values in the GEOM_EXTRA_TABLE category labelled with a matching value of A, B or C. ; data_geom_table_headnote_ loop_ _name '_geom_table_headnote_A' '_geom_table_headnote_B' '_geom_table_headnote_C' _category geom_extra_tables _type char _definition ; Head note for a printed table of arbitrary geometric quantities. This should not be used in the tabulation of standard geometric properties (use instead the categories GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND, GEOM_TORSION), but is a useful device for creating and annotating printed tables. The label A, B or C is implicitly associated with a list of geometric values in the GEOM_EXTRA_TABLE category labelled with a matching value of A, B or C. ; ################ ## GEOM_HBOND ## ################ data_geom_angle_DHA _name '_geom_angle_DHA' _category geom_hbond _type numb _type_conditions esd _related_item '_geom_hbond_angle_DHA' _related_function replace _units deg _units_detail 'degrees' _definition ; Unofficial data name for the angle in degrees defined by the three sites _geom_bond_atom_site_label_D, *_H and *_A. Site at *_D (the hydrogen atom participating in the interaction) is at the apex of the angle. Found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_bond_atom_site_label_A _name '_geom_bond_atom_site_label_A' _category geom_hbond _type char _related_item '_geom_hbond_atom_site_label_A' _related_function replace _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; Unofficial data name for the atom site label of the acceptor atom participating in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_bond_atom_site_label_D _name '_geom_bond_atom_site_label_D' _category geom_hbond _type char _related_item '_geom_hbond_atom_site_label_D' _related_function replace _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; Unofficial data name for the atom site label of the donor atom participating in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_bond_atom_site_label_H _name '_geom_bond_atom_site_label_H' _category geom_hbond _type char _related_item '_geom_hbond_atom_site_label_H' _related_function replace _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; Unofficial data name for the atom site label of the hydrogen atom participating in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_bond_distance_DH _name '_geom_bond_distance_DH' _category geom_hbond _type numb _type_conditions esd _related_item '_geom_hbond_distance_DH' _related_function replace _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; Unofficial data name for the distance in angstroms between the donor and hydrogen sites in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_contact_distance_DA _name '_geom_contact_distance_DA' _category geom_hbond _type numb _type_conditions esd _related_item '_geom_hbond_distance_DA' _related_function replace _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; Unofficial data name for the distance in angstroms between the donor and acceptor sites in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_contact_distance_HA _name '_geom_contact_distance_HA' _category geom_hbond _type numb _type_conditions esd _related_item '_geom_hbond_distance_HA' _related_function replace _enumeration_range 0.0: _units A _units_detail 'angstroms' _definition ; Unofficial data name for the distance in angstroms between the hydrogen and acceptor sites in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_contact_site_symmetry_A _name '_geom_contact_site_symmetry_A' _category geom_hbond _type char _related_item '_geom_hbond_site_symmetry_A' _related_function replace loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; Unofficial data name for the symmetry code of an atom site participating in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_contact_site_symmetry_D _name '_geom_contact_site_symmetry_D' _category geom_hbond _type char _related_item '_geom_hbond_site_symmetry_D' _related_function replace loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; Unofficial data name for the symmetry code of an atom site participating in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; data_geom_contact_site_symmetry_H _name '_geom_contact_site_symmetry_H' _category geom_hbond _type char _related_item '_geom_hbond_site_symmetry_H' _related_function replace loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; Unofficial data name for the symmetry code of an atom site participating in a hydrogen bond, found in CIFs submitted for publication before version 2 of the core CIF dictionary. ; ########## ## PUBL ## ########## # This would really have been better in the journal category data_publ_vrn_code _name '_publ_vrn_code' _category publ _type char _definition ; The Validation Report Number, an identifier added to CIFs that have been handled by an IUCr journals Validation Editor. ; ################# ## PUBL_OBJECT ## ################# data_publ_object_[] _name '_publ_object_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _iucr_publ_object.id _iucr_publ_object.type _iucr_publ_object.content 1 cif ; sin \q/\l ; 2 tex ; \sin {\theta \over \lambda} ; ; ; Example 1 - hypothetical example demonstrating alternative markup for a mathematical expression using the CIF markup convention, and TeX, respectively. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; 'Reserved' items for IUCr in-house development of 'objects' that cannot otherwise be included in text fields to be stored in the CIF and referenced from within text fields. As of this version, these are highly experimental and should not be considered as a model for other applications. ; data_iucr_publ_object.content _name '_iucr_publ_object.content' _category publ_object _type char _list yes _list_reference '_iucr_publ_object.id' _definition ; The content of the object. ; data_iucr_publ_object.id _name '_iucr_publ_object.id' _category publ_object _type char _list yes _list_mandatory yes _definition ; Code identifying an object. ; data_iucr_publ_object.type _name '_iucr_publ_object.type' _category publ_object _type char _list yes _list_reference '_iucr_publ_object.id' _definition ; The data type of the object. It is expected that any future elaborated definition will specify enumerated type codes. ; ####################### ## PUBLCIF_DATABLOCK ## ####################### data_publcif_datablock_[] _name '_publcif_datablock_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; data_I _publcif_datablock.id '{657f18b0-826a-425f-99c7}' ; ; Example 1 - hypothetical example where data block 'I' is given a unique identifier '{657f18b0-826a-425f-99c7}' to provide a reference to be used by items in the PUBLCIF_INFO_DATABLOCK and PUBLCIF_INFO_TABLES categories. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; 'Private' data items used by the IUCr publCIF software for housekeeping purposes. Data items in this category are used to store information about the parent data block. ; data_publcif_datablock.id _name '_publcif_datablock.id' _category publcif_datablock _type char _definition ; A data block identifier maintained by publCIF to allow relationships between data blocks to be managed elsewhere (e.g. by data items in the PUBLCIF_INFO_DATABLOCK and PUBLCIF_INFO_TABLES categories). The use of this private identifier guards against normalization of the original data block codes (e.g. to establish uniqueness in a collection of separate CIFs, or to aid publication workflow). ; ###################### ## PUBLCIF_INFO_CIF ## ###################### data_publcif_info_cif_[] _name '_publcif_info_cif_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _publcif_info_cif.paper_type 'EE' ; ; Example 1 - the article derived from this CIF is to be typeset in the style of Acta Cryst. Section E "Research Communications" (the actual codes used are maintained internally to publCIF and not tabulated in this dictionary). ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; For use by publCIF - to store information about the type of document to be generated from the parent data block (i.e. that containing 'global' data items). ; data_publcif_info_cif.paper_type _name '_publcif_info_cif.paper_type' _category publcif_info_cif _type char _definition ; For use by publCIF - application-specific codes relating to different article styles (in terms of content and formatting). ; ############################ ## PUBLCIF_INFO_DATABLOCK ## ############################ data_publcif_info_datablock_[] _name '_publcif_info_datablock_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publcif_info_datablock.id _publcif_info_datablock.publ_exptl _publcif_info_datablock.publ_geom _publcif_info_datablock.structure "{657f18b0-826a-425f-99c7}" ? ? n "{f682b772-6196-4139-93e8}" y y y "{2d76c7aa-a8e1-427b-8571}" n n y ; ; Example 1 - hypothetical example for a CIF containing three data blocks, of which two contain structural data and of these the experimental and geometry data in only one block (referenced by {f682b772-6196-4139-93e8}) are to appear in the final publication. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; 'Private' data items used by the IUCr publCIF software for housekeeping purposes. As of this version they are specific to aspects of style and presentation in IUCr journals, and are best ignored or discarded by anyone else. They are treated as 'global' items spanning all blocks within the CIF. ; data_publcif_info_datablock.id _name '_publcif_info_datablock.id' _category publcif_info_datablock _type char _list yes _list_mandatory yes _definition ; Code identifying the data block to which the formatting directives in the PUBLCIF_INFO_DATABLOCK category apply. The ordering of block codes defines the order in which the data are presented in the published article. ; data_publcif_info_datablock.publ_exptl _name '_publcif_info_datablock.publ_exptl' _category publcif_info_datablock _type char _list yes _list_mandatory no _list_reference '_publcif_info_datablock.id' loop_ _enumeration _enumeration_detail no 'do not publish experimental data' n 'abbreviation for "no"' yes 'do publish experimental data' y 'abbreviation for "yes"' _enumeration_default y _definition ; This code signals whether the experimental data should be published for the structure described in the referenced data block. ; data_publcif_info_datablock.publ_geom _name '_publcif_info_datablock.publ_geom' _category publcif_info_datablock _type char _list yes _list_mandatory no _list_reference '_publcif_info_datablock.id' loop_ _enumeration _enumeration_detail no 'do not publish geometry data' n 'abbreviation for "no"' yes 'do publish geometry data' y 'abbreviation for "yes"' _enumeration_default y _definition ; This code signals whether the molecular geometry data should be published for the structure described in the referenced data block. ; data_publcif_info_datablock.structure _name '_publcif_info_datablock.structure' _category publcif_info_datablock _type char _list yes _list_mandatory no _list_reference '_publcif_info_datablock.id' loop_ _enumeration _enumeration_detail no 'does not contain structural data' n 'abbreviation for "no"' yes 'does contain structural data' y 'abbreviation for "yes"' _enumeration_default y _definition ; This code signals whether the referenced data block contains structural data. ; ############################## ## PUBLCIF_INFO_EXPTL_TABLE ## ############################## data_publcif_info_exptl_table_[] _name '_publcif_info_exptl_table_max_cols_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _publcif_info_exptl_table_max_cols 4 _publcif_info_exptl_table_use_headnotes n ; ; Example 1 - directives to a typesetting routine to layout an experimental table with a maximum of 4 columns of structural data per table group and no printed head notes. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; For use by publCIF - to store information about the layout of the table of experimental details to be included in a document derived from the parent CIF (i.e. 'global' data items). ; data_publcif_info_exptl_table_max_cols _name '_publcif_info_exptl_table_max_cols' _category publcif_info_exptl_table _type numb _enumeration_range 0: _enumeration_default 0 _definition ; Defines how a multistructure table will be split into table groups. Its usual implementation specifies the number of columns, each summarising the experimental details from one structure, that may span a page width in the published article. The default value of '0' is special and is understood as 'impose no grouping' - i.e. include all structures in a single multi-column table. ; data_publcif_info_exptl_table_use_headnotes _name '_publcif_info_exptl_table_use_headnotes' _category publcif_info_exptl_table _type char _definition ; For use by publCIF - flags the printing of headnotes associated with an experimental table in an autogenerated article. ; #################################### ## PUBLCIF_INFO_EXPTL_TABLE_EXTRA ## #################################### data_publcif_info_exptl_table_extra_[] _name '_publcif_info_exptl_table_extra_[]' _category category_overview _type null _definition ; 'Private' data items used by the IUCr publcif software for housekeeping purposes. As of this version they are specific to aspects of style and presentation in IUCr journals, and are best ignored or discarded by anyone else. ; data_publcif_info_exptl_table_extra_item _name '_publcif_info_exptl_table_extra_item' _category publcif_info_exptl_table_extra _type char _list yes _definition ; Specifies additional experimental data items to be published (in cases where they are not usually requested). ; ##################################### ## PUBLCIF_INFO_EXPTL_TABLE_HEADER ## ##################################### data_publcif_info_exptl_table_header_[] _name '_publcif_info_exptl_table_header_[]' _category category_overview _type null _definition ; 'Private' data items used by the IUCr publcif software for housekeeping purposes. As of this version they are specific to aspects of style and presentation in IUCr journals, and are best ignored or discarded by anyone else. ; data_publcif_info_exptl_table_header_item _name '_publcif_info_exptl_table_header_item' _category publcif_info_exptl_table_header _type char _list yes _definition ; Specifies which items to use for column headings in the published table of experimental data. ; ######################### ## PUBLCIF_INFO_TABLES ## ######################### data_publcif_info_tables_[] _name '_publcif_info_tables_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publcif_info_tables.block_id _publcif_info_tables.reference_item "{657f18b0-826a-425f-99c7}" "_publcif_info_datablock.publ_exptl" "{f682b772-6196-4139-93e8}" "_geom_bond_atom_site_label_1" "{2d76c7aa-a8e1-427b-8571}" "_geom_bond_atom_site_label_1" "{f682b772-6196-4139-93e8}" "_geom_hbond_atom_site_label_D" "{2d76c7aa-a8e1-427b-8571}" "_geom_hbond_atom_site_label_D" ; ; Example 1 - hypothetical example where bond length and hydrogen-bond distance tables from two structures are to be included in the article generated from the CIF. There is also a pointer to a data structure used internally to locate experimental tables that are to be published (e.g. in a certain category of article). ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; For use by publCIF - to store information about the tables to be included in a document derived from the parent CIF (i.e. 'global' data items). ; data_publcif_info_tables.block_id _name '_publcif_info_tables.block_id' _category publcif_info_tables _type char _list yes _list_mandatory yes _definition ; For use by publCIF to locate data blocks containing tabular material to be printed, e.g. in certain article categories. ; data_publcif_info_tables.reference_item _name '_publcif_info_tables.reference_item' _category publcif_info_tables _type char _list yes _list_mandatory no _list_reference '_publcif_info_tables.block_id' _definition ; For use by publCIF to identify the geometry and other tables to be printed, e.g. in certain article categories. ; ######################## ## PUBLCIF_JMOLSCRIPT ## ######################## data_publcif_jmolscript_[] _name '_publcif_jmolscript_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _publcif_jmolscript.group _publcif_jmolscript.id _publcif_jmolscript.model _publcif_jmolscript.model_type _publcif_jmolscript.type _publcif_jmolscript.type_group _publcif_jmolscript.caption _publcif_jmolscript.script fig1 . 1 o jmolApplet . 'Asymmetric unit of silver bis(1H-imidazolium) trinitrate.' ; # Jmol state version 11.5.37 2008-04-29 08:46; # fullName = "jmolApplet0__339102683804489__"; # ... function _setWindowState(); # height 494; # width 494; stateVersion = 1105037; ... end function; function _setFileState(); ... ; ; ; Example 1 - Structure of an enhanced figure stored in publcif as 'fig1'. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; 'Private' data items used by the IUCr publcif software to store jmolscript commands allowing interactive visualization of the molecular structure reported in the CIF by the application Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ ; data_publcif_jmolscript.caption _name '_publcif_jmolscript.caption' _category publcif_jmolscript _type char _list yes _list_reference '_publcif_jmolscript.id' _definition ; Descriptive caption accompanying a Jmol enhanced figure. ; data_publcif_jmolscript.group _name '_publcif_jmolscript.group' _category publcif_jmolscript _type char _list yes _list_reference '_publcif_jmolscript.id' _example 'fig1' _definition ; Code grouping together related visualization scripts. ; data_publcif_jmolscript.id _name '_publcif_jmolscript.id' _category publcif_jmolscript _type char _list yes _list_mandatory yes _definition ; Code identifying a Jmol enhanced figure. ; data_publcif_jmolscript.model _name '_publcif_jmolscript.model' _category publcif_jmolscript _type numb _list yes _list_reference '_publcif_jmolscript.id' _enumeration_range 1: _enumeration_default 1 _definition ; The numeric identifier of the structural model in the CIF to which the Jmol visualization will apply. ; data_publcif_jmolscript.model_type _name '_publcif_jmolscript.model_type' _category publcif_jmolscript _type char _list yes _list_reference '_publcif_jmolscript.id' loop_ _enumeration _enumeration_detail i inorganic m macromolecular o organic _definition ; Type of structural model - inorganic, organic or biological macromolecular. ; data_publcif_jmolscript.script _name '_publcif_jmolscript.script' _category publcif_jmolscript _type numb _list yes _list_reference '_publcif_jmolscript.id' _definition ; The actual script commands to be evaluated by Jmol. ; data_publcif_jmolscript.type _name '_publcif_jmolscript.type' _category publcif_jmolscript _type numb _list yes _list_reference '_publcif_jmolscript.id' _definition ; Type of Jmol script. ; data_publcif_jmolscript.type_group _name '_publcif_jmolscript.type_group' _category publcif_jmolscript _type numb _list yes _list_reference '_publcif_jmolscript.id' _definition ; Code grouping together related Jmol scripts. ; ############ ## REFINE ## ############ data_iucr_refine_instruction_details _name '_iucr_refine_instruction_details' _category refine _type char _related_item '_iucr_refine_instructions_details' _related_function replace _definition ; Used to store refinement-software instructions listings. This data name was advertised in journal Notes for Authors in error for _iucr_refine_instructions_details; it is formally deprecated and appears here only for validation of legacy files. It should NOT be written by future CIF generators/editors. ; data_iucr_refine_instructions_details _name '_iucr_refine_instructions_details' _category refine _type char _related_item '_iucr_refine_instruction_details' _related_function alternate _definition ; Used to store refinement-software instructions listings. Requested specifically by journal editors to record the instructions executed by specific programs in the last least-squares refinement cycle, allowing validation of the reported structure model. Typically a verbatim input file (e.g. in SHELXL .ins format); The value is therefore treated as a raw string (i.e. no CIF markup). Use of this feature in IUCr journals is seen as an interim measure; the preferred long-term approach is the development of software able to handle data items in the CIF restraints dictionary. ; data_iucr_refine_instructions_details_constraints _name '_iucr_refine_instructions_details_constraints' _category refine _type char _definition ; Used to store refinement-software instructions listings. Some software packages find it useful to process listings of refinement constraints and restraints separately. This item and its companion *_restraints are provided for the benefit of such packages. The general data item _iucr_refine_instructions_details may also be used. Use of this feature in IUCr journals is seen as an interim measure; the preferred long-term approach is the development of software able to handle data items in the CIF restraints dictionary. ; data_iucr_refine_instructions_details_restraints _name '_iucr_refine_instructions_details_restraints' _category refine _type char _definition ; Used to store refinement-software instructions listings. Some software packages find it useful to process listings of refinement constraints and restraints separately. This item and its companion *_constraints are provided for the benefit of such packages. The general data item _iucr_refine_instructions_details may also be used. Use of this feature in IUCr journals is seen as an interim measure; the preferred long-term approach is the development of software able to handle data items in the CIF restraints dictionary. ; ######### ## VRF ## ######### data_vrf_[] _name '_vrf_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _vrf_REFLT_03_I ; PROBLEM: Alert B: < 90% complete (theta max?) RESPONSE: Data provided according to standard protocols of service crystallography laboratory: 91.4% complete at theta = 25.0\% ; ; ; Example 1 - Autogenerated alert created by checkCIF and responded to by author. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Data items in the validation report form (VRF) category record information relevant to the handling of validation alerts during the journal review procedure. For ease of handling, arbitrary datanames of the type _vrf_*_" are permitted for an author to insert a response to a validation alert, where * = test name; " = data-block identifier. It is not possible to tabulate all possible datanames of this type. The prefix "vrf" has been registered with the IUCr as a reserved dataname prefix. ; data_vrf_VALIDATOR_comments _name '_vrf_VALIDATOR_comments' _category vrf _type char _example 'No apparent missed symmetry.' _definition ; Textual commentary by journal Validation Editor on author response to validation alerts. ;