############################################################################## # # # CIF RESTRAINTS AND CONSTRAINTS DICTIONARY VERSION 1.0 # # ----------------------------------------------------- # # # # This dictionary contains the names and definitions proposed for reporting # # restraints and constraints in the Core CIF dictionary # # # # Copyright 2011 International Union of Crystallography # ############################################################################## ############################################################################## # # # Some notes on the philosophy followed in this dictionary # # -------------------------------------------------------- # # The items in this dictionary are designed for reporting the restraints # # and constraints applied during the final refinement of a structure. # # They are not intended, nor are they suitable, for use as instructions # # to a refinement program. # # # # A RESTRAINT is a condition used in the refinement of a crystal structure # # that requires one or more of the parameters of the refinement to lie # # within a certain range. # # # # A CONSTRAINT is a condition used in the refinement of a crystal structure # # that requires one or more parameters of the refinement to have a # # specific value or be exactly equal to another refined parameter. # # # # The range of values allowed in a restraint is given in this dictionary # # by a target value and a weighting parameter, the latter being the # # expectation value of the difference between the refined value and # # the target. Constraints are indicated by setting the weighting # # parameter to zero. # # # # Restraints and constraints are handled in many different ways in different # # programs. The actual parameters restrained are determined by the way the # # restraint is expressed within the program, and different programs # # express the same restraint in different ways. In this dictionary the # # restraints are expressed in a way that is most natural to the description # # of the crystal structure, which means that the parameters given here # # may not correspond to the parameters that were actually restrained. # # For example, the rigid-body constraint is expressed here by listing the # # atoms in the rigid body. Distances and angles between them are constant. # # For a rigid body the target parameters are the same as the refined # # parameters, allowing the target geometry of the rigid body to be found # # from the reported atomic coordinates. However, in order to apply # # this constraint in a refinement, either the coordinates of the atoms # # in some arbitrary coordinate system or a sufficient number of geometric # # parameters of the body must be specified. Since all these methods # # preserve the rigid body intact, it is only the result that needs to be # # reported, not the details of the method used. In this way the description # # of restraints and constraints has been kept as simple as possible. # # # # The restraints and constraints used are many and varied, and not all # # can be given in the forms listed in this dictionary. # # For this reason a general item _restr_special_details has been # # provided so that a text description can be given for # # a restraint or constraint that cannot be reported in any other way. # # # # Attention is drawn to existing items in the core dictionary that flag # # whether items have been restrained or constrained: # # _atom_site_refinement_flags_adp # # _atom_site_refinement_flags_occupation # # _atom_site_refinement_flags_posn # # _atom_site_restraints # # # ############################################################################## data_on_this_dictionary _dictionary_name cif_core_restraints.dic _dictionary_version 1.0 _dictionary_update 2011-03-09 _dictionary_history ; 2009-18-10 Following consultations between the user community and I. David Brown and Ilia Guzei, IDB started preparing this dictionary using DDL1 by creating items required by distance and angle restraints. 2009-12-09 IDB Completed first draft. 2010-01-13 IDB Corrected minor errors detected by IG prior to DMG review. 2010-01-14 IDB: Run through vcif by Brian McMahon and corrections made. esd replaced by su in _type_conditions. 2010-06-03 IDB: U_ISO, U_SIMIILAR. 2010-09-15 IDB: The revised rigid body description is added. 2010-10-15 IDB: Corrections from H. Bernstein made. 2010-12-09 NJA: minor editing. 2011-01-24 BMcM: minor editing incorporating authors' final revisions. 2011-03-09 BMcM: released ; # This dictionary describes 14 restraints some of which are also constraints. # # 1. Other restraint or constraint # 2. Angle # 3. Distance # 4. Minimum approach of two atoms # 5. Angles restrained to be equal # 6. Distances restrained to be equal # 7. Torsion angles restrained to be equal # 8. Restrained parameter # 9. Rigid body # 10. Atoms lie on a plane # 11. Torsion angle # 12. Isotropic atom # 13. Rigid bond # 14. Similar atomic displacement parameters # # ---------------------------------------------------------------------------- # RESTRAINT 1. GENERAL RESTRAINT # ---------------------------------------------------------------------------- # A general description of constraints and restraints not covered # by other CIF items. # ###################### # # # RESTR # # # ###################### data_restr_[] _name '_restr_[]' _category category_overview _type null _definition ; This category is for describing restraints that cannot be described elsewhere. ; data_restr_special_details _name '_restr_special_details' _category restr _type char _definition ; Text describing any restraint or constraint that cannot be described using any of the the other restraint items. See also _atom_site_restraints. ; # # ---------------------------------------------------------------------------- # RESTRAINT 2. AN ANGLE IS RESTRAINED TO A PREDETERMINED VALUE. # ---------------------------------------------------------------------------- # #################### # # # RESTR_ANGLE # # # #################### data_restr_angle_[] _name '_restr_angle_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_angle_atom_site_label_1 _restr_angle_site_symmetry_1 _restr_angle_atom_site_label_2 _restr_angle_atom_site_label_3 _restr_angle_site_symmetry_3 _restr_angle_target _restr_angle_target_weight_param _restr_angle_diff _restr_angle_details C1 1_555 C2 C3 1_555 120 1 -0.3 'generated by JANA' C2 1_555 C3 C4 3_455 120 1.5 0.5 ? ; ; Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Items in this category define angles that were restrained in the final refinement. ; data_restr_angle_atom_site_label_ loop_ _name '_restr_angle_atom_site_label_1' '_restr_angle_atom_site_label_2' '_restr_angle_atom_site_label_3' _category restr_angle _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels used to define the angle. Atom 2 is at the apex of the angle. ; data_restr_angle_details _name '_restr_angle_details' _category restr_angle _type char _list yes _list_reference '_restr_angle_atom_site_label_' _definition ; A free-text description of the restraint. ; data_restr_angle_diff _name '_restr_angle_diff' _category restr_angle _type numb _type_conditions su _list yes _list_reference '_restr_angle_atom_site_label_' _enumeration_range 0: _units degrees _definition ; The difference between the target and the refined angle. ; data_restr_angle_site_symmetry_ loop_ _name '_restr_angle_site_symmetry_1' '_restr_angle_site_symmetry_2' '_restr_angle_site_symmetry_3' _category restr_angle _type char _list yes _list_reference '_restr_angle_atom_site_label_' _enumeration_default 1_555 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 ; The symmetry transformation needed to generate the coordinates of the three atoms that define the angle. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_restr_angle_target _name '_restr_angle_target' _category restr_angle _type numb _list yes _list_reference '_restr_angle_atom_site_label_' _enumeration_range 0:180 _units degrees _definition ; The expectation angle defined by the three atoms. This is the target angle for the restrained refinement. ; data_restr_angle_target_weight_param _name '_restr_angle_target_weight_param' _category restr_angle _type numb _list yes _list_reference '_restr_angle_atom_site_label_' _enumeration_range 0:180 _enumeration_default 0 _units degrees _definition ; Weighting parameter = sqrt(1/weight). It is the expectation value of the difference between the refined value and the target. If this parameter is set to zero, the angle will be constrained to refine to the target value. If this item is absent, its value will be taken as zero and the distance will be constrained. ; # # ---------------------------------------------------------------------------- # RESTRAINT 3. A DISTANCE IS RESTRAINED TO A PREDETERMINED VALUE. # ---------------------------------------------------------------------------- # ##################### # # # RESTR_DISTANCE # # # ##################### data_restr_distance_[] _name '_restr_distance_[]' _category category_overview _type null _definition ; This category describes restraints applied to distances during the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_distance_atom_site_label_1 _restr_distance_atom_site_label_2 _restr_distance_site_symmetry_2 _restr_distance_target _restr_distance_target_weight_param _restr_distance_diff _restr_distance_details C1 C2 1_555 1.524 0.04 -0.032 'generated by SHELX DFIX' C2 C3 1_555 1.340 0.04 0.051 'generated by SHELX DFIX' Na1 Ca1 1_555 0.0 0.0 0.0 'Na1 is constrained to occupy Ca site' Fe1 Ca1 1_555 0.0 0.0 0.0 ? Al1 Ca1 1_555 0.0 0.0 0.0 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_distance_atom_site_label_ loop_ _name '_restr_distance_atom_site_label_1' '_restr_distance_atom_site_label_2' _category restr_distance _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels of the two atoms defining the distance restrained. ; data_restr_distance_details _name '_restr_distance_details' _category restr_distance _type char _list yes _list_reference '_restr_distance_atom_site_label_' _definition ; A free-text description of the restraint. ; data_restr_distance_diff _name '_restr_distance_diff' _category restr_distance _type numb _type_conditions su _list yes _list_reference '_restr_distance_atom_site_label_' _units A _units_detail Angstrom _definition ; The difference between the target and the refined distance. ; data_restr_distance_site_symmetry_ loop_ _name '_restr_distance_site_symmetry_1' '_restr_distance_site_symmetry_2' _category restr_distance _type char _list yes _list_reference '_restr_distance_atom_site_label_' 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' _enumeration_default 1_555 _definition ; The symmetry transformation needed to generate the coordinates of the two atoms that define the distance. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the distance. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_restr_distance_target _name '_restr_distance_target' _category restr_distance _type numb _list yes _list_reference '_restr_distance_atom_site_label_' _units A _units_detail Angstrom _definition ; The expectation distance between the two atoms. This is the target distance for the restrained refinement. ; data_restr_distance_target_weight_param _name '_restr_distance_target_weight_param' _category restr_distance _type numb _list yes _list_reference '_restr_distance_atom_site_label_' _enumeration_default 0 _units A _units_detail Angstrom _definition ; Weighting parameter = sqrt(1/weight). It is the expectation value of the difference between the refined value and the target. If this parameter is set to zero, the distance will be constrained to refine to the target value. If this item is absent, its value will be taken as zero and the distance will be constrained. ; # # ---------------------------------------------------------------------------- # RESTRAINT 4. ATOMS CANNOT OCCUPY THE SAME POSITION # ---------------------------------------------------------------------------- # The 'anti-bumping' restraint prevents two atoms from occupying the # same site. It would normally be reported only for those distances # in which this restraint was invoked. # ########################### # # # RESTR_DISTANCE_MIN # # # ########################### data_restr_distance_min_[] _name '_restr_distance_min_[]' _category category_overview _type null _definition ; Items in this category offer power-law and exponential expressions for a function designed to prevent two atoms occupying the same location. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_distance_min_atom_site_label_1 _restr_distance_min_site_symmetry_1 _restr_distance_min_atom_site_label_2 _restr_distance_min_site_symmetry_2 _restr_distance_min_A _restr_distance_min_B _restr_distance_min_C _restr_distance_min_E _restr_distance_min_F _restr_distance_min_G _restr_distance_min_distance _restr_distance_min_details O1 1_555 O2 1_555 0 . . 1 2.8 0.3 2.75(1) 'using the exponential restraint' O2 1_555 O3 2_455 0 0 0 1 2.8 0 2.83(1) 'using the hard sphere model' ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_distance_min_A _name '_restr_distance_min_A' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _enumeration_range 0: _enumeration_default 0 _definition ; The weight associated with the difference between the refined distance D and the prescribed minimum distance (B or F) is given by the expression w = A*(B/D)^C^ + E*exp((D-F)/G) A and E are dimensionless weighting parameters. Either function could be used alone by setting A or E to zero. The default values of A and E are zero. If A=0, B and C are undefined; if E=0, F and G are undefined. A hard-sphere contact can be generated by setting E=1, F=prescribed minimum distance and G=0. In this case G (combined with a non-zero E) should be treated as a flag indicating a hard-sphere interaction with a target distance of F so as to avoid division by zero. ; data_restr_distance_min_atom_site_label_ loop_ _name '_restr_distance_min_atom_site_label_1' '_restr_distance_min_atom_site_label_2' _category restr_distance_min _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels for the two atoms that are kept apart. ; data_restr_distance_min_B _name '_restr_distance_min_B' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _enumeration_range 0: _enumeration_default 0 _units A _units_detail Angstrom _definition ; The weight associated with the difference between the refined distance D and the prescribed minimum distance (B or F) is given by the expression w = A*(B/D)^C^ + E*exp((D-F)/G) A and E are dimensionless weighting parameters. Either function could be used alone by setting A or E to zero. The default values of A and E are zero. If A=0, B and C are undefined; if E=0, F and G are undefined. A hard-sphere contact can be generated by setting E=1, F=prescribed minimum distance and G=0. In this case G (combined with a non-zero E) should be treated as a flag indicating a hard-sphere interaction with a target distance of F so as to avoid division by zero. ; data_restr_distance_min_C _name '_restr_distance_min_C' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _definition ; The weight associated with the difference between the refined distance D and the prescribed minimum distance (B or F) is given by the expression w = A*(B/D)^C^ + E*exp((D-F)/G) A and E are dimensionless weighting parameters. Either function could be used alone by setting A or E to zero. The default values of A and E are zero. If A=0, B and C are undefined; if E=0, F and G are undefined. A hard-sphere contact can be generated by setting E=1, F=prescribed minimum distance and G=0. In this case G (combined with a non-zero E) should be treated as a flag indicating a hard-sphere interaction with a target distance of F so as to avoid division by zero. ; data_restr_distance_min_details _name '_restr_distance_min_details' _category restr_distance_min _type char _list yes _list_reference 'restr_distance_min_atom_site_label_' _definition ; A text description of the restraint giving details not given elsewhere. ; data_restr_distance_min_difference _name '_restr_distance_min_difference' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _units A _units_detail Angstrom _definition ; The difference in angstroms between the refined distance of approach of the two atoms and the target distance B or F: difference = D - B or D - F ; data_restr_distance_min_distance _name '_restr_distance_min_distance' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The refined distance, D, between the two atoms. ; data_restr_distance_min_E _name '_restr_distance_min_E' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _enumeration_default 0 _definition ; The weight associated with the difference between the refined distance D and the prescribed minimum distance (B or F) is given by the expression w = A*(B/D)^C^ + E*exp((D-F)/G) A and E are dimensionless weighting parameters. Either function could be used alone by setting A or E to zero. The default values of A and E are zero. If A=0, B and C are undefined; if E=0, F and G are undefined. A hard-sphere contact can be generated by setting E=1, F=prescribed minimum distance and G=0. In this case G (combined with a non-zero E) should be treated as a flag indicating a hard-sphere interaction with a target distance of F so as to avoid division by zero. ; data_restr_distance_min_F _name '_restr_distance_min_F' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The weight associated with the difference between the refined distance D and the prescribed minimum distance (B or F) is given by the expression w = A*(B/D)^C^ + E*exp((D-F)/G) A and E are dimensionless weighting parameters. Either function could be used alone by setting A or E to zero. The default values of A and E are zero. If A=0, B and C are undefined; if E=0, F and G are undefined. A hard-sphere contact can be generated by setting E=1, F=prescribed minimum distance and G=0. In this case G (combined with a non-zero E) should be treated as a flag indicating a hard-sphere interaction with a target distance of F so as to avoid division by zero. ; data_restr_distance_min_G _name '_restr_distance_min_G' _category restr_distance_min _type numb _list yes _list_reference 'restr_distance_min_atom_site_label_' _units A _units_detail Angstrom _definition ; The weight associated with the difference between the refined distance D and the prescribed minimum distance (B or F) is given by the expression w = A*(B/D)^C^ + E*exp((D-F)/G) A and E are dimensionless weighting parameters. Either function could be used alone by setting A or E to zero. The default values of A and E are zero. If A=0, B and C are undefined; if E=0, F and G are undefined. A hard-sphere contact can be generated by setting E=1, F=prescribed minimum distance and G=0. In this case G (combined with a non-zero E) should be treated as a flag indicating a hard-sphere interaction with a target distance of F so as to avoid division by zero. ; data_restr_distance_min_site_symmetry_ loop_ _name '_restr_distance_min_site_symmetry_1' '_restr_distance_min_site_symmetry_2' _category restr_distance_min _type char _list yes _list_reference 'restr_distance_min_atom_site_label_' _definition ; The site symmetries of the two atoms kept apart. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 atoms that are kept apart. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; # # ---------------------------------------------------------------------------- # RESTRAINT 5. SEVERAL ANGLES ARE RESTRAINED TO BE EQUAL. # ---------------------------------------------------------------------------- # This restraint contains two categories. # The first defines the angles restrained and assigns # them to different classes that are restrained independently. # The second category defines the properties of each class. # ########################## # # # RESTR_EQUAL_ANGLE # # # ########################## data_restr_equal_angle_[] _name '_restr_equal_angle_[]' _category category_overview _type null _definition ; Items in this category list the atoms defining the angles that are restrained to be equal in the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_equal_angle_atom_site_label_1 _restr_equal_angle_site_symmetry_1 _restr_equal_angle_atom_site_label_2 # Atom 2 is at the apex of the angle _restr_equal_angle_site_symmetry_2 _restr_equal_angle_atom_site_label_3 _restr_equal_angle_site_symmetry_3 _restr_equal_angle_class_id _restr_equal_angle_detail C1 1_555 C2 1_555 C3 1_555 1 'Benzene ring with mirror symmetry' C2 1_555 C3 1_555 C4 2_655 2 ? C4 1_555 C5 1_555 C6 1_555 2 ? C5 1_555 C6 1_555 C1 1_555 1 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_equal_angle_atom_site_label_ loop_ _name '_restr_equal_angle_atom_site_label_1' '_restr_equal_angle_atom_site_label_2' '_restr_equal_angle_atom_site_label_3' _category restr_equal_angle _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels of the three atoms that define one of the angles restrained to be equal to other angles in the same class. ; data_restr_equal_angle_class_id _name '_restr_equal_angle_class_id' _category restr_equal_angle _type char _list yes _list_reference '_restr_equal_angle_atom_site_label_' _enumeration_default 1 _definition ; A character string identifying the class of equal angles to which this angle belongs. ; data_restr_equal_angle_details _name '_restr_equal_angle_detail' _category restr_equal_angle _type char _list yes _list_reference '_restr_equal_angle_atom_site_label_' _definition ; A text description giving details of an angle in a class of angles that are restrained to be equal. ; data_restr_equal_angle_site_symmetry_ loop_ _name '_restr_equal_angle_site_symmetry_1' '_restr_equal_angle_site_symmetry_2' '_restr_equal_angle_site_symmetry_3' _category restr_equal_angle _type char _list yes _list_reference '_restr_equal_angle_atom_site_label_' 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' _enumeration_default 1_555 _definition ; The site symmetries of the three atoms that define an angle restrained to be equal to other angles in the same class. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ################################### # # # RESTR_EQUAL_ANGLE_CLASS # # # ################################### data_restr_equal_angle_class_[] _name '_restr_equal_angle_class_[]' _category category_overview _type null _definition ; Items in this category give details of the target angles for each class of angles that are restrained to be equal in the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_equal_angle_class_class_id _restr_equal_angle_class_target_weight_param _restr_equal_angle_class_average _restr_equal_angle_class_esd _restr_equal_angle_class_diff_max _restr_equal_angle_class_detail 1 0.50 123.52 0.32 0.62 ? 2 0.50 118.23 0.52 1.43 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_equal_angle_class_average _name '_restr_equal_angle_class_average' _category restr_equal_angle_class _type numb _list yes _list_reference '_restr_equal_angle_class_class_id' _enumeration_range 0: _units degrees _definition ; The average angle in the class of angles restrained to be the same after refinement. ; data_restr_equal_angle_class_class_id _name '_restr_equal_angle_class_class_id' _category restr_equal_angle_class _type char _list yes _list_mandatory yes _list_link_parent '_restr_equal_angle_class_id' _enumeration_default 1 _definition ; A character string that identifies the class of angles whose properties are described. ; data_restr_equal_angle_class_detail _name '_restr_equal_angle_class_detail' _category restr_equal_angle_class _type char _list yes _list_reference '_restr_equal_angle_class_class_id' _definition ; A text description giving details of the class of angles that are restrained to be equal. ; data_restr_equal_angle_class_diff_max _name '_restr_equal_angle_class_diff_max' _category restr_equal_angle_class _type numb _type_conditions su _list yes _list_reference '_restr_equal_angle_class_class_id' _enumeration_range 0: _units degrees _definition ; The maximum deviation of an angle in the class from the class average after refinement. ; data_restr_equal_angle_class_esd _name '_restr_equal_angle_class_esd' _category restr_equal_angle_class _type numb _list yes _list_reference '_restr_equal_angle_class_class_id' _enumeration_range 0: _units degrees _definition ; The actual estimated standard deviation of the angles in the class from their average after refinement. This number is expected to be similar to the value set for _restr_equal_angle_class_target_weight_param. ; data_restr_equal_angle_class_target_weight_param _name '_restr_equal_angle_class_target_weight_param' _category restr_equal_angle_class _type numb _list yes _list_reference '_restr_equal_angle_class_class_id' _enumeration_range 0: _enumeration_default 0 _units degrees _definition ; The weighting parameter = sqrt(1/weight). The expectation value of the estimated standard deviation of the angles in the class from their average after refinement. This value determines the weight assigned to the restraint. If it is zero the angles are constrained to be equal. The default value is zero. ; # # ---------------------------------------------------------------------------- # RESTRAINT 6. SEVERAL DISTANCES ARE RESTRAINED TO BE EQUAL. # ---------------------------------------------------------------------------- # This restraint contains two categories. # The first defines the distances restrained and assigns # them to different classes that are restrained independently. # The second category defines the properties of each class. # ############################# # # # RESTR_EQUAL_DISTANCE # # # ############################# data_restr_equal_distance_[] _name '_restr_equal_distance_[]' _category category_overview _type null _definition ; Items in this category list the atoms defining the distances that are restrained to be equal in the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_equal_distance_atom_site_label_1 _restr_equal_distance_site_symmetry_1 _restr_equal_distance_atom_site_label_2 _restr_equal_distance_site_symmetry_2 _restr_equal_distance_class_id _restr_equal_distance_details C1 1_555 C2 1_555 1 'C1-C2 and C3-C4 are restrained to be equal' C2 1_555 C3 1_555 2 'C2-C3, C4-C5 and C5-C6 are restrained to be equal' C3 1_555 C4 2_655 1 ? C4 1_555 C5 1_555 2 ? C5 1_555 C6 1_555 2 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_equal_distance_atom_site_label_ loop_ _name '_restr_equal_distance_atom_site_label_1' '_restr_equal_distance_atom_site_label_2' _category restr_equal_distance _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels of the two atoms that define one of the distances restrained to be equal to other distances in the same class. ; data_restr_equal_distance_class_id _name '_restr_equal_distance_class_id' _category restr_equal_distance _type char _list yes _list_reference '_restr_equal_distance_atom_site_label_' _enumeration_default 1 _definition ; A character string identifying the class of equal distances to which this distance belongs. ; data_restr_equal_distance_details _name '_restr_equal_distance_details' _category restr_equal_distance _type char _list yes _list_reference '_restr_equal_distance_atom_site_label_' _definition ; A text description giving details of a distance in a class of distances that are restrained to be equal. ; data_restr_equal_distance_site_symmetry_ loop_ _name '_restr_equal_distance_site_symmetry_1' '_restr_equal_distance_site_symmetry_2' _category restr_equal_distance _type char _list yes _list_reference '_restr_equal_distance_atom_site_label_' 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' _enumeration_default 1_555 _definition ; The site symmetries of the two atoms that define a distance restrained to be equal to other distances in the same class. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the distance. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ################################### # # # RESTR_EQUAL_DISTANCE_CLASS # # # ################################### data_restr_equal_distance_class_[] _name '_restr_equal_distance_class_[]' _category category_overview _type null _definition ; Items in this category give details of the target distances for each class of distances that are restrained to be equal in the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_equal_distance_class_class_id _restr_equal_distance_class_target_weight_param _restr_equal_distance_class_average _restr_equal_distance_class_esd _restr_equal_distance_class_diff_max _restr_equal_distance_class_details 1 0.04 1.534 0.032 0.053 ? 2 0.04 1.338 0.052 0.103 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_equal_distance_class_average _name '_restr_equal_distance_class_average' _category restr_equal_distance_class _type numb _list yes _list_reference '_restr_equal_distance_class_class_id' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The average distance in the class of distances restrained to be the same after refinement. ; data_restr_equal_distance_class_class_id _name '_restr_equal_distance_class_class_id' _category restr_equal_distance_class _type char _list yes _list_mandatory yes _list_link_parent '_restr_equal_distance_class_id' _enumeration_default 1 _definition ; A character string that identifies the class of distances whose properties are described. ; data_restr_equal_distance_class_details _name '_restr_equal_distance_class_details' _category restr_equal_distance_class _type char _list yes _list_reference '_restr_equal_distance_class_class_id' _definition ; A text description giving details of the class of distances that are restrained to be equal. ; data_restr_equal_distance_class_diff_max _name '_restr_equal_distance_class_diff_max' _category restr_equal_distance_class _type numb _type_conditions su _list yes _list_reference '_restr_equal_distance_class_class_id' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The maximum deviation of a distance in the class from the class average after refinement. ; data_restr_equal_distance_class_esd _name '_restr_equal_distance_class_esd' _category restr_equal_distance_class _type numb _list_reference '_restr_equal_distance_class_class_id' _list yes _enumeration_range 0: _units Angstrom _definition ; The actual estimated standard deviation of the distances in the class from their average after refinement. This number is expected to be similar to the value set for _restr_equal_distance_class_target_weight_param. ; data_restr_equal_distance_class_target_weight_param _name '_restr_equal_distance_class_target_weight_param' _category restr_equal_distance_class _type numb _list yes _list_reference '_restr_equal_distance_class_class_id' _enumeration_range 0: _enumeration_default 0 _units A _units_detail Angstrom _definition ; The weighting parameter = sqrt(1/weight). The expectation value of the estimated standard deviation of the distances in the class from their average after refinement. This value determines the weight assigned to the restraint. If it is zero the distances are constrained to be equal. The default value is zero. ; # # ---------------------------------------------------------------------------- # RESTRAINT 7. SEVERAL TORSION ANGLES ARE RESTRAINED TO BE EQUAL. # ---------------------------------------------------------------------------- # This restraint contains two categories. # The first defines the torsion angles restrained and assigns # them to different classes that are restrained independently. # The second category defines the properties of each class. # ############################ # # # RESTR_EQUAL_TORSION # # # ############################ data_restr_equal_torsion_[] _name '_restr_equal_torsion_[]' _category category_overview _type null _definition ; Items in this category list the atoms defining the torsion angles that are restrained to be equal in the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_equal_torsion_atom_site_label_1 _restr_equal_torsion_site_symmetry_1 _restr_equal_torsion_atom_site_label_2 _restr_equal_torsion_site_symmetry_2 _restr_equal_torsion_atom_site_label_3 _restr_equal_torsion_site_symmetry_3 _restr_equal_torsion_atom_site_label_4 _restr_equal_torsion_site_symmetry_4 _restr_equal_torsion_class_id _restr_equal_torsion_details C1 1_555 C2 1_555 C3 1_555 C4 1_555 1 ? C5 1_555 C6 1_555 C1 1_555 C2 1_555 1 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_equal_torsion_atom_site_label_ loop_ _name '_restr_equal_torsion_atom_site_label_1' '_restr_equal_torsion_atom_site_label_2' '_restr_equal_torsion_atom_site_label_3' '_restr_equal_torsion_atom_site_label_4' _category restr_equal_torsion _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels of the four atoms that define one of the torsion angles restrained to be equal to other torsion angles in the same class. The torsion angle is the dihedral angle between the plane defined by atoms 1, 2 and 3, and the plane defined by atoms 2, 3 and 4. ; data_restr_equal_torsion_class_id _name '_restr_equal_torsion_class_id' _category restr_equal_torsion _type char _list yes _list_reference '_restr_equal_torsion_atom_site_label_' _enumeration_default 1 _definition ; A character string identifying the class of equal torsion angles to which this torsion angle belongs. ; data_restr_equal_torsion_details _name '_restr_equal_torsion_details' _category restr_equal_torsion _type char _list yes _list_reference '_restr_equal_torsion_atom_site_label_' _definition ; A text description giving details of a torsion angle in a class of torsion angles that are restrained to be equal. ; data_restr_equal_torsion_site_symmetry_ loop_ _name '_restr_equal_torsion_site_symmetry_1' '_restr_equal_torsion_site_symmetry_2' '_restr_equal_torsion_site_symmetry_3' '_restr_equal_torsion_site_symmetry_4' _category restr_equal_torsion _type char _list yes _list_reference '_restr_equal_torsion_atom_site_label_' _enumeration_default 1_555 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 ; The site symmetries of the four atoms that define a torsion angle restrained to be equal to other torsion angles in the same class. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the torsion angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; ################################### # # # RESTR_EQUAL_TORSION_CLASS # # # ################################### data_restr_equal_torsion_class_[] _name '_restr_equal_torsion_class_[]' _category category_overview _type null _definition ; Items in this category give details of the target torsion angles for each class of torsion angles that are restrained to be equal in the final refinement. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_equal_torsion_class_class_id _restr_equal_torsion_class_target_weight_param _restr_equal_torsion_class_average _restr_equal_torsion_class_esd _restr_equal_torsion_class_diff_max _restr_equal_torsion_class_details 1 0.50 123.52 0.32 0.62 ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_equal_torsion_class_average _name '_restr_equal_torsion_class_average' _category restr_equal_torsion_class _type numb _list yes _list_reference '_restr_equal_torsion_class_class_id' _enumeration_range 0: _units degrees _definition ; The average torsion angle in the class of torsion angles restrained to be the same after refinement. ; data_restr_equal_torsion_class_class_id _name '_restr_equal_torsion_class_class_id' _category restr_equal_torsion_class _type char _list yes _list_mandatory yes _list_link_parent '_restr_equal_torsion_class_id' _enumeration_default 1 _definition ; A character string that identifies the class of torsion angles whose properties are described. ; data_restr_equal_torsion_class_details _name '_restr_equal_torsion_class_details' _category restr_equal_torsion_class _type char _list yes _list_reference '_restr_equal_torsion_class_class_id' _definition ; A text description giving details of the class of torsion angles that are restrained to be equal. ; data_restr_equal_torsion_class_diff_max _name '_restr_equal_torsion_class_diff_max' _category restr_equal_torsion_class _type numb _type_conditions su _list yes _list_reference '_restr_equal_torsion_class_class_id' _enumeration_range 0: _units degrees _definition ; The maximum deviation of a torsion angle in the class from the class average after refinement. ; data_restr_equal_torsion_class_esd _name '_restr_equal_torsion_class_esd' _category restr_equal_torsion_class _type numb _list yes _list_reference '_restr_equal_torsion_class_class_id' _enumeration_range 0: _units degrees _definition ; The actual estimated standard deviation of the torsion angles in the class from their average after refinement. This number is expected to be similar to the value set for _restr_equal_torsion_class_target_weight_param. ; data_restr_equal_torsion_class_target_weight_param _name '_restr_equal_torsion_class_target_weight_param' _category restr_equal_torsion_class _type numb _list yes _list_reference '_restr_equal_torsion_class_class_id' _enumeration_range 0: _enumeration_default 0 _units degrees _definition ; The weighting parameter = sqrt(1/weight). This is the expectation value of the estimated standard deviation (given in _restr_equal_torsion_class_esd) of the torsion angles in the class from their average after refinement. This value determines the weight assigned to the target. If it is zero the torsion angles are constrained to be equal. The default value is zero. ; # # ---------------------------------------------------------------------------- # RESTRAINT 8. THE SUM OF A GIVEN PARAMETER OF THE SPECIFIED ATOMS IS # RESTRAINED. # ---------------------------------------------------------------------------- # This restraint, which will normally be used to restrain the total # occupancy of an atom site, can be used to restrain the value of # SUM(over the specified atoms){PARAMETER*COEFFICIENT} # where PARAMETER will usually be the occupancy # (but other allowed quantities such as x, y and z will be specified # in the enumeration list) and COEFFICIENT is a user-defined # number with a default value of 1.0. # Two loops are needed to describe this restraint. # ######################## # # # RESTR_PARAMETER # # # ######################## data_restr_parameter_[] _name '_restr_parameter_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_parameter_id _restr_parameter_class_id _restr_parameter_atom_site_label _restr_parameter_atom_coefficient 1 1 O1 1 2 1 O1a 1 3 1 O1b 1 ; ; These examples should be read in conjunction with the examples given for the category restr_parameter_class. Example 1. In class 1 the sites O1, O1a and O1b refer to separate sites over which oxygen is disordered, but which in total contain 0.8 oxygen atoms (as defined by _restr_parameter_class_target). ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_parameter_id _restr_parameter_class_id _restr_parameter_atom_site_label _restr_parameter_atom_coefficient a 2 Na1 1 b 2 K1 1 c 2 Ca1 1 d 2 Al1 1 ; ; Example 2. Class 2 consists of a mixture of Na, K, Ca and Al atoms on the same site with the total occupancy set to 1.0 as defined in _restr_parameter_class_target. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_parameter_id _restr_parameter_class_id _restr_parameter_atom_site_label _restr_parameter_atom_coefficient 1 3 Na1 1 2 3 K1 1 3 3 Ca1 2 4 3 Al1 3 ; ; Example 3. Class 3 consists of the same atoms as class 2, but by using coefficients equal to the ionic charge, the total charge on the site is restrained to 2.0. Note that the parameter restrained is still the occupancy but the use of coefficients transforms the restraint from occupancy to formal charge. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_parameter_id _restr_parameter_class_id _restr_parameter_atom_site_label _restr_parameter_atom_coefficient 1 4 O2 1 ; ; Example 4. In class 4 the y coordinate of O2 is restrained to be close to a pseudo-mirror plane at y = 0.5 (see _restr_parameter_class_target). This example may not have much practical use, but is included to show what can be done with this definition. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_parameter_id _restr_parameter_class_id _restr_parameter_atom_site_label _restr_parameter_atom_coefficient 1 5 O3 1 2 5 O4 1 ; ; Example 5. In class 5 the positions of O3 and O4 are correlated in such a way that these atoms are displaced equal distances from the plane x = 0 [i.e., x(O3) + x(O4) = 0]. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; This restraint, which will normally be used to restrain the total occupancy of an atom site, can be used to restrain the value of SUM(over the specified atoms){PARAMETER*COEFFICIENT} where PARAMETER will usually be the value of the occupancy (but other allowed quantities such as x, y and z can be specified in the enumeration) and COEFFICIENT is a user-defined number with a default value of 1.0. The restraint requires two loops; the first defines the atoms in each sum (class) and the second describes the properties of the class. ; data_restr_parameter_atom_coefficient _name '_restr_parameter_atom_coefficient' _category restr_parameter _type numb _list yes _list_reference '_restr_parameter_id' _enumeration_default 1 _definition ; A parameter that scales the quantity being restrained. It can be used to convert a constraint on occupancy to a constraint on ionic charge. ; data_restr_parameter_atom_site_label _name '_restr_parameter_atom_site_label' _category restr_parameter _type char _list yes _list_reference '_restr_parameter_id' _list_link_parent '_atom_site_label' _definition ; The atom-site label for an atom in this class. ; data_restr_parameter_class_id _name '_restr_parameter_class_id' _category restr_parameter _type char _list yes _list_reference '_restr_parameter_id' _enumeration_default 1 _definition ; The identifier of the class of restraint applied to the atoms. ; data_restr_parameter_id _name '_restr_parameter_id' _category restr_parameter _type char _list yes _list_mandatory yes _definition ; A unique identifier for each line in a loop. ; ################################### # # # RESTR_PARAMETER_CLASS # # # ################################### data_restr_parameter_class_[] _name '_restr_parameter_class_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_parameter_class_class_id _restr_parameter_class_parameter_type _restr_parameter_class_target _restr_parameter_class_target_weight_param _restr_parameter_class_details 1 occupancy 0.8 0.01 'total occupation is 0.8' 2 occupancy 1.0 0.001 'total occupation is 1.0' 3 occupancy 2.0 0.01 'total charge is 2.0' 4 position_y 0.5 0.002 'keep close to pseudo-mirror plane' 5 position_x 0 0.01 'correlate position of O3 and O4' ; ; Example 1. This example gives the properties of the five classes given as examples in restr_parameter. The _*_class_id is the _list_reference and is the same as _*_class_id in the restr_parameter loop. The _*_parameter_type indicates the atomic parameter that is restrained. _*_target is the target value for the sum of the product of _restr_parameter_atom_coefficient and the value of the _*_parameter_type for the atom. _*_target_weight_sum gives the expectation value of the difference between the target and the refined value of sum(coefficient*parameter). _*_details gives a description of the restraint applied. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; This restraint, which will normally be used to restrain the total occupancy of an atom site, can be used to restrain the value of SUM(over the specified atoms){PARAMETER*COEFFICIENT} where PARAMETER will usually be the value of the occupancy (but other allowed quantities such as x, y and z can be specified in the enumeration) and COEFFICIENT is a user-defined number with a default value of 1.0. The restraint requires two loops, the first defines the atoms in each sum (class) and the second describes the properties of the class. ; data_restr_parameter_class_class_id _name '_restr_parameter_class_class_id' _category restr_parameter_class _type char _list yes _list_mandatory yes _list_link_parent '_restr_parameter_class_id' _enumeration_default 1 _definition ; The class ID of the restraint described in this category. ; data_restr_parameter_class_details _name '_restr_parameter_class_details' _category restr_parameter_class _type char _list yes _list_reference '_restr_parameter_class_class_id' _definition ; A text description of the restraint. ; data_restr_parameter_class_parameter_type _name '_restr_parameter_class_parameter_type' _category restr_parameter_class _type char _list yes _list_reference '_restr_parameter_class_class_id' loop_ _enumeration _enumeration_detail occupancy '_atom_site_occupancy' position_x '_atom_site_fract_x' position_y '_atom_site_fract_y' position_z '_atom_site_fract_z' _definition ; A flag that indicates the nature of the value that is being restrained. ; data_restr_parameter_class_target _name '_restr_parameter_class_target' _category restr_parameter_class _type numb _list yes _list_reference '_restr_parameter_class_class_id' _definition ; The target value for the sum of values of the appropriate parameter type multiplied by the _*_target_weight_param. ; data_restr_parameter_class_target_weight_param _name '_restr_parameter_class_target_weight_param' _category restr_parameter_class _type numb _list yes _list_reference '_restr_parameter_class_class_id' _enumeration_default 0 _definition ; Weighting parameter = sqrt(1/weight). It is the expectation value of the difference between the refined value of the sum(parameter*coefficient) and the _*_target. If this parameter is set to zero, the sum will be constrained to refine to the target value. If this item is absent, its value will be taken as zero and the distance will be constrained. ; # # ---------------------------------------------------------------------------- # RESTRAINT 9. A GROUP OF ATOMS IS RESTRAINED TO LIE ON A PLANE. # ---------------------------------------------------------------------------- # This restraint contains two categories. # The first lists the atoms that define each plane, each plane being # composed of atoms from the same class. # The second category describes the properties of each plane (class). # ###################### # # # RESTR_PLANE # # # ###################### data_restr_plane_[] _name '_restr_plane_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_plane_id _restr_plane_atom_site_label _restr_plane_site_symmetry _restr_plane_class_id _restr_plane_target_weight_param _restr_plane_displacement _restr_plane_details 1 c1 1_555 1 0.02 0.002(1) 'c1 to c4 lie on one plane' 2 c2 1_555 1 0.02 -0.003(2) ? 3 c3 1_555 1 0.02 -0.002(1) ? 4 c4 1_555 1 0.02 0.002(2) ? 5 c1 2_655 2 0.003 0.004(1) 'c1, c5, c6 and c7 lie on one plane' 6 c5 1_555 2 0.003 -0.002(2) ? 7 c6 1_555 2 0.003 0.002(3) ? 8 c7 1_555 2 0.003 -0.002(2) ? ; ;Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Items in this category define the atoms that make up each class of plane. ; data_restr_plane_atom_site_label _name '_restr_plane_atom_site_label' _category restr_plane _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; An atom-site label of one of the atoms that form the plane. ; data_restr_plane_class_id _name '_restr_plane_class_id' _category restr_plane _type char _list yes _list_mandatory yes _list_reference '_restr_plane_id' _enumeration_default 1 _definition ; A character string that identifies the plane to which this atom is constrained. ; data_restr_plane_details _name '_restr_plane_details' _category restr_plane _type char _list yes _list_reference '_restr_plane_id' _definition ; A text string giving details not described elsewhere. ; data_restr_plane_displacement _name '_restr_plane_displacement' _category restr_plane _type numb _type_conditions su _list yes _list_reference '_restr_plane_id' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The distance between this atom and the best plane through all the atoms. ; data_restr_plane_id _name '_restr_plane_id' _category restr_plane _type char _list yes _list_mandatory yes _enumeration_default 1 _definition ; A unique identifier for each line in the list. ; data_restr_plane_site_symmetry _name '_restr_plane_site_symmetry' _category restr_plane _type char _list yes _list_mandatory yes _list_reference '_restr_plane_id' _enumeration_default 1_555 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 ; The site symmetry of the atom that helps to define the plane to which it is restrained. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the plane. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_restr_plane_target_weight_param _name '_restr_plane_target_weight_param' _category restr_plane _type numb _list yes _list_reference '_restr_plane_id' _enumeration_range 0: _enumeration_default 0.0 _units A _units_detail Angstrom _definition ; The weighting parameter = sqrt(1/weight). The expectation value of the distance in angstroms between this atom and the best plane through all the atoms of the class. ; ############################ # # # RESTR_PLANE_CLASS # # # ############################ data_restr_plane_class_[] _name '_restr_plane_class_[]' _category category_overview _type null _definition ; Items in this category describe the properties of the different groups of atoms that are restrained to form a plane. ; loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_plane_class_class_id _restr_plane_class_displacement_esd _restr_plane_class_displacement_max_atom_site_label _restr_plane_class_displacement_max_site_symmetry _restr_plane_class_displacement_max _restr_plane_class_details 1 0.032 c2 1_555 0.094 'displacements for plane 1' 2 0.0021 c1 2_655 0.010 'displacements for plane 2' ; ; Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data_restr_plane_class_class_id _name '_restr_plane_class_class_id' _category restr_plane_class _type char _list yes _list_mandatory yes _list_link_parent '_restr_plane_class_id' _enumeration_default 1 _definition ; The class identifier for the plane whose properties are described. ; data_restr_plane_class_details _name '_restr_plane_class_details' _category restr_plane_class _type char _list yes _list_reference '_restr_plane_class_class_id' _definition ; Text describing any special features of the restraint. ; data_restr_plane_class_displacement_esd _name '_restr_plane_class_displacement_esd' _category restr_plane_class _type char _list yes _list_reference '_restr_plane_class_class_id' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The observed estimated standard deviation of the atoms from this plane. ; data_restr_plane_class_displacement_max _name '_restr_plane_class_displacement_max' _category restr_plane_class _type numb _type_conditions su _list yes _list_reference '_restr_plane_class_class_id' _enumeration_range 0: _units A _units_detail Angstrom _definition ; The distance in angstroms from the plane to the atom furthest removed from the plane. ; data_restr_plane_class_displacement_max_atom_site_label _name '_restr_plane_class_displacement_max_atom_site_label' _category restr_plane_class _type char _list yes _list_reference '_restr_plane_class_class_id' _list_link_parent '_atom_site_label' _definition ; The atom-site label of the atom that lies furthest from the plane defined by this class. ; data_restr_plane_class_displacement_max_site_symmetry _name '_restr_plane_class_displacement_max_site_symmetry' _category restr_plane_class _type char _list yes _list_reference '_restr_plane_class_class_id' _enumeration_default 1_555 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 ; The site symmetry of the atom lying furthest from the plane to which it is restrained. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 furthest from the plane. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; # # ---------------------------------------------------------------------------- # RESTRAINT 10. ATOMS ARE DEFINED AS BELONGING TO RIGID BODIES. # ---------------------------------------------------------------------------- # ############################# # # # RESTR_RIGID_BODY # # # ############################# data_restr_rigid_body_[] _name '_restr_rigid_body_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_rigid_body_id _restr_rigid_body_atom_site_label _restr_rigid_body_site_symmetry _restr_rigid_body_class_id _restr_rigid_body_details 1 C1 1_555 1 ? 2 C2 1_555 1 ? 3 C3 1_555 1 'C3 is a hinge atom' 4 C4 1_555 1 'C4 is a hinge atom' 5 C3 1_555 2 ? 6 C4 1_555 2 ? 7 C5 2_555 2 ? 8 C6 1_555 2 ? ; ; Example 1. The first rigid body contains C1, C2, C3 and C4, the second rigid body contains C3, C4, C5 and C6. The bond between C3 and C4 is common to both rigid bodies. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Items in this category list the atoms defining one or more bodies that are constrained to be rigid in the final refinement. This is done by listing the atom-site label and symmetry operation for each atom in each rigid body. Since rigid bodies are only constrained, not restrained, the rigid body is adequately defined by the refined coordinate in the atom_site list. A second category, restr_rigid_body_class, permits a description of each rigid body to be given in a *_details item. ; data_restr_rigid_body_id _name '_restr_rigid_body_id' _category restr_rigid_body _type char _list yes _list_mandatory yes _definition ; A unique identifier for each atom in the list of atoms in the RESTR_RIGID_BODY category. ; data_restr_rigid_body_class_id _name '_restr_rigid_body_class_id' _category restr_rigid_body _type char _list yes _list_reference '_restr_rigid_body_id' _enumeration_default 1 _definition ; A character string identifying a rigid body. ; data_restr_rigid_body_atom_site_label _name '_restr_rigid_body_atom_site_label' _category restr_rigid_body _type char _list yes _list_reference '_restr_rigid_body_id' _list_link_parent '_atom_site_label' _definition ; The atom-site labels of an atom in a rigid body. ; data_restr_rigid_body_site_symmetry_ _name '_restr_rigid_body_site_symmetry' _category restr_rigid_body _type char _list yes _list_reference '_restr_rigid_body_id' loop_ _example _example_detail . 'no symmetry or translation applied' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +1 on x; -1 on y' _enumeration_default 1_555 _definition ; The site symmetry of an atom in a rigid body. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match the number given in _space_group_symop_id (formerly _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 in calculating the rigid body. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_restr_rigid_body_details _name '_restr_rigid_body_details' _category restr_rigid_body _type char _list yes _list_reference '_restr_rigid_body_id' _definition ; A text description giving details of a rigid body in a class of rigid bodies that are constrained to be equal. ; ################################### # # # RESTR_RIGID_BODY_CLASS # # # ################################### data_restr_rigid_body_class_[] _name '_restr_rigid_body_class_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_rigid_body_class_class_id _restr_rigid_body_class_details 1 'Phenyl ring' 2 'methyl group' ; ; Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Items in this category give details of the different rigid bodies as defined by _restr_rigid_body_class_id ; data_restr_rigid_body_class_class_id _name '_restr_rigid_body_class_class_id' _category restr_rigid_body_class _type char _list yes _list_mandatory yes _list_link_parent '_restr_rigid_body_class_id' _enumeration_default 1 _definition ; A character string that identifies the rigid body. It must match one of the values of _restr_rigid_body_class_id. ; data_restr_rigid_body_class_details _name '_restr_rigid_body_class_details' _category restr_rigid_body_class _type char _list yes _list_reference '_restr_rigid_body_class_class_id' _definition ; A text description giving details of a rigid body. ; # ---------------------------------------------------------------------------- # RESTRAINT 11. A TORSION ANGLE IS CONSTRAINED TO A PREDETERMINED VALUE # ---------------------------------------------------------------------------- # ###################### # # # RESTR_TORSION # # # ###################### data_restr_torsion_[] _name '_restr_torsion_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; _restr_torsion_atom_site_label_1 _restr_torsion_site_symmetry_1 _restr_torsion_atom_site_label_2 _restr_torsion_site_symmetry_2 _restr_torsion_atom_site_label_3 _restr_torsion_site_symmetry_3 _restr_torsion_atom_site_label_4 _restr_torsion_site_symmetry_4 _restr_torsion_angle_target _restr_torsion_weight_param _restr_torsion_diff _restr_torsion_details Na1 1_555 Na1 2_555 O1 2_555 H101 1_555 90 1 0.97 ? ; ; Example 1. An example of a torsion angle restrained to 90+/-1 degree with a refined difference of 0.97 degrees. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; Items in this category define torsion angles that were restrained in the final refinement. ; data_restr_torsion_angle_target _name '_restr_torsion_angle_target' _category restr_torsion _type numb _list yes _list_reference '_restr_torsion_atom_site_label_' _enumeration_range -180:180 _units degree _definition ; The angle in degrees to which the torsion angle is restrained. The torsion angle is the dihedral angle between the plane defined by atoms 1, 2 and 3, and the plane defined by atoms 2, 3 and 4. ; data_restr_torsion_atom_site_label_ loop_ _name '_restr_torsion_atom_site_label_1' '_restr_torsion_atom_site_label_2' '_restr_torsion_atom_site_label_3' '_restr_torsion_atom_site_label_4' _category restr_torsion _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels of the atoms in the sequence in which they are linked by the bonds whose torsion angle is to be restrained. ; data_restr_torsion_details _name '_restr_torsion_details' _category restr_torsion _type numb _list yes _list_reference '_restr_torsion_atom_site_label_' _units degree _definition ; A free-text description of the restraint. ; data_restr_torsion_diff _name '_restr_torsion_diff' _category restr_torsion _type numb _type_conditions su _list yes _list_reference '_restr_torsion_atom_site_label_' _units degree _definition ; The difference between the target and the refined torsion angle. ; data_restr_torsion_site_symmetry_ loop_ _name '_restr_torsion_site_symmetry_1' '_restr_torsion_site_symmetry_2' '_restr_torsion_site_symmetry_3' '_restr_torsion_site_symmetry_4' _category restr_torsion _type char _list yes _list_reference '_restr_torsion_atom_site_label_' 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' _enumeration_default 1_555 _definition ; The symmetry transformations needed to generate the coordinates of the four atoms that define the torsion angle. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the torsion angle. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_restr_torsion_weight_param _name '_restr_torsion_weight_param' _category restr_torsion _type numb _list yes _list_reference '_restr_torsion_atom_site_label_' _enumeration_range 0: _enumeration_default 0 _units degree _definition ; Weighting parameter = sqrt(1/weight). It is the expectation value of the difference between the refined value and the target. If this parameter is set to zero, the angle will be constrained to refine to the target value. If this item is absent, its value will be taken as zero and the angle will be constrained. ; # # ---------------------------------------------------------------------------- # RESTRAINT 12: THE ATOMIC DISPLACEMENT PARAMETER IS RESTRAINED TO BE # ISOTROPIC. # ---------------------------------------------------------------------------- # ##################### # # # RESTR_U_ISO # # # ##################### data_restr_U_iso_[] _name '_restr_U_iso_[]' _category category_overview _type null _list_reference '_restr_U_iso_atom_site_label' loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_U_iso_atom_site_label _restr_U_iso_weight_param Na1 0.003 O3 0.008 O8 0.008 ; ; Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; This restraint attempts to make an anisotropic atomic displacement isotropic within the range of the weighting parameter. It corresponds to SHELX ISO. ; data_restr_U_iso_atom_site_label _name '_restr_U_iso_atom_site_label' _category restr_U_iso _type char _list yes _list_reference '_restr_U_iso_atom_site_label' _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; Label of the atom whose atomic displacement parameters are restrained. ; data_restr_U_iso_weight_param _name '_restr_U_iso_weight_param' _category restr_U_iso _type numb _list yes _list_reference '_restr_U_iso_atom_site_label' _enumeration_range 0: _enumeration_default 0 _units A^-2^ _units_detail 'reciprocal Angstrom squared' _definition ; The expectation value of the difference between the refined and the isotropic equivalent of the anisotropic atomic displacement parameters. The default value of zero indicates a constraint. ; # # ---------------------------------------------------------------------------- # RESTRAINT 13. ADPs ARE RESTRAINED FOR A RIGID BOND. # ---------------------------------------------------------------------------- # This "rigid bond" restraint restrains the anisotropic displacement # parameters of two atoms so that they are equal within a certain # _weight_param along the direction of the vector joining the atoms. # ###################### # # # RESTR_U_RIGID # # # ###################### data_restr_U_rigid_[] _name '_restr_U_rigid_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_U_rigid_atom_site_label_1 _restr_U_rigid_site_symmetry_1 _restr_U_rigid_atom_site_label_2 _restr_U_rigid_site_symmetry_2 _restr_U_rigid_target_weight_param _restr_U_rigid_U_parallel _restr_U_rigid_diff _restr_U_rigid_details C1 1_555 C2 2_655 0.001 0.0023(2) 0.0006 'C1-C2 is a rigid bond' ; ; Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; The items in this category restrains the anisotropic displacement parameters of two atoms to be equal within a certain *_target_weight_param along the direction of the vector joining the atoms. ; data_restr_U_rigid_atom_site_label_ loop_ _name '_restr_U_rigid_atom_site_label_1' '_restr_U_rigid_atom_site_label_2' _category restr_U_rigid _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The atom-site labels of the two atoms that define the rigid bond. ; data_restr_U_rigid_details _name '_restr_U_rigid_details' _category restr_U_rigid _type char _list yes _list_reference '_restr_U_rigid_atom_site_label_' _definition ; Free-text information about the rigid-bond restraint. ; data_restr_U_rigid_diff _name '_restr_U_rigid_diff' _category restr_U_rigid _type numb _type_conditions su _list yes _list_reference 'restr_U_rigid_atom_site_label_' _units A^-2^ _units_detail Angstrom^-2^ _definition ; The difference between the components along the bond direction of the atomic displacement parameters, U, of the two atoms. ; data_restr_U_rigid_site_symmetry_ loop_ _name '_restr_U_rigid_site_symmetry_1' '_restr_U_rigid_site_symmetry_2' _category restr_U_rigid _type char _list yes _list_reference 'restr_U_rigid_atom_site_label_' _enumeration_default 1_555 _definition ; The site symmetries of the two atoms that define the rigid bond. The symmetry code of each atom site is given as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id (formerly _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 in calculating the rigid bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; 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' data_restr_U_rigid_target_weight_param _name '_restr_U_rigid_target_weight_param' _category restr_U_rigid _type numb _list yes _list_reference '_restr_U_rigid_atom_site_label_' _enumeration_default 0 _units A^-2^ _units_detail Angstrom^-2^ _definition ; The weighting parameter = sqrt(1/weight). The expectation value of the difference between the components of the atomic displacement parameter, U, along the bond direction of the two atoms that define the bond. This number is used to assign a weight during refinement. A value of zero causes the restraint to become a constraint. This item has a default value of zero. ; data_restr_U_rigid_U_parallel _name '_restr_U_rigid_U_parallel' _category restr_U_rigid _type numb _list yes _list_reference '_restr_U_rigid_atom_site_label_' _enumeration_default 0 _units A^-2^ _units_detail Angstrom^-2^ _definition ; The average value of the components parallel to the bond of the atomic displacement parameters of the two atoms that define the bond. ; # # ---------------------------------------------------------------------------- # RESTRAINT 14. TWO ATOMS ARE RESTRAINED TO HAVE THE SAME ADPs. # ---------------------------------------------------------------------------- # ##################### # # # RESTR_U_SIMILAR # # # ##################### data_restr_U_similar_[] _name '_restr_U_similar_[]' _category category_overview _type null loop_ _example _example_detail # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; loop_ _restr_U_similar_atom_site_label_1 _restr_U_similar_atom_site_label_2 _restr_U_similar_weight_param C1 C2 0.08 C2 C3 0.08 ; ; Example 1. ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _definition ; This category forces the atomic displacement ellipsoids of atom 2 to be equal to that of atom 1 within the range of the weighting parameter. This is the same as SHELX SIMU. ; data_restr_U_similar_atom_site_label_ loop_ _name '_restr_U_similar_atom_site_label_1' '_restr_U_similar_atom_site_label_2' _category restr_U_similar _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; _restr_U_similar_atom_site_label_1 is the atom-site label of the atom whose atomic displacement parameters are used as the target. _restr_U_similar_atom_site_label_2 is the atom-site label of the atom whose atomic displacement parameters are restrained to be the same as atom 1. ; data_restr_U_similar_weight_param _name '_restr_U_similar_weight_param' _category restr_U_similar _type numb _list yes _list_reference '_restr_U_similar_atom_site_label_' _enumeration_range 0: _enumeration_default 0 _units A^-2^ _units_detail 'reciprocal Angstrom squared' _definition ; The expectation value of the difference between the anisotropic atomic displacement parameters of the two atoms. The default value of zero represents a constraint. ; # -------------- End of restraint and constraint dictionary -------------