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cif_rstr.dic
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#\#CIF_2.0
##############################################################################
# #
# CIF RESTRAINTS AND CONSTRAINTS DICTIONARY VERSION 1.0 #
# ----------------------------------------------------- #
# #
# This dictionary contains the names and definitions for reporting #
# restraints and constraints in the Core CIF dictionary. #
# #
# #
##############################################################################
data_CIF_RSTR
_dictionary.title CIF_RSTR
_dictionary.class Instance
_dictionary.version 3.1.1
_dictionary.date 2024-05-15
_dictionary.uri www.iucr.org/cif/dic/cif_rstr.dic
_dictionary.ddl_conformance 3.11.09
_dictionary.namespace CifRstr
_description.text
;
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
;
save_CIF_RSTR
_definition.id CIF_RSTR
_definition.scope Category
_definition.class Head
_definition.update 2024-05-15
_description.text
;
The CIF_RSTR group contains the definitions of data items that
are used to restrain and constrain crystallographic parameters.
;
_name.category_id CIF_DIC
_name.object_id CIF_RSTR
_import.get
[
{'dupl':Ignore 'file':cif_core.dic 'mode':Full 'save':CIF_CORE_HEAD}
]
save_
save_RESTR
_definition.id RESTR
_definition.scope Category
_definition.class Set
_definition.update 2014-06-29
_description.text
;
This category is for describing restraints that cannot be
described elsewhere.
;
_name.category_id CIF_RSTR
_name.object_id RESTR
save_
save_restr.special_details
_definition.id '_restr.special_details'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_special_details'
_description.text
;
Text describing any restraint or constraint that cannot be
described using any of the the other restraint items.
See also _atom_site_restraints.
;
_name.category_id restr
_name.object_id special_details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_RESTR_ANGLE
_definition.id RESTR_ANGLE
_definition.scope Category
_definition.class Loop
_definition.update 2014-06-29
_description.text
;
Items in this category define angles that were restrained
in the final refinement. Atom 2 is at the apex of the angle.
;
_name.category_id CIF_RSTR
_name.object_id RESTR_ANGLE
loop_
_category_key.name
'_restr_angle.atom_site_label_1'
'_restr_angle.site_symmetry_1'
'_restr_angle.atom_site_label_2'
'_restr_angle.site_symmetry_2'
'_restr_angle.atom_site_label_3'
'_restr_angle.site_symmetry_3'
save_
save_restr_angle.atom_site_label_1
_definition.id '_restr_angle.atom_site_label_1'
loop_
_alias.definition_id
'_restr_angle_atom_site_label_1'
_name.category_id restr_angle
_name.object_id atom_site_label_1
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_angle.atom_site_label_2
_definition.id '_restr_angle.atom_site_label_2'
loop_
_alias.definition_id
'_restr_angle_atom_site_label_2'
_name.category_id restr_angle
_name.object_id atom_site_label_2
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_angle.atom_site_label_3
_definition.id '_restr_angle.atom_site_label_3'
loop_
_alias.definition_id
'_restr_angle_atom_site_label_3'
_name.category_id restr_angle
_name.object_id atom_site_label_3
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_angle.details
_definition.id '_restr_angle.details'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_angle_details'
_description.text
;
A free-text description of the restraint.
;
_name.category_id restr_angle
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_restr_angle.diff
_definition.id '_restr_angle.diff'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_angle_diff'
_description.text
;
The difference between the target and the refined angle.
;
_name.category_id restr_angle
_name.object_id diff
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code degrees
save_
save_restr_angle.site_symmetry_1
_definition.id '_restr_angle.site_symmetry_1'
loop_
_alias.definition_id
'_restr_angle_site_symmetry_1'
_name.category_id restr_angle
_name.object_id site_symmetry_1
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_angle.site_symmetry_2
_definition.id '_restr_angle.site_symmetry_2'
loop_
_alias.definition_id
'_restr_angle_site_symmetry_2'
_name.category_id restr_angle
_name.object_id site_symmetry_2
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_angle.site_symmetry_3
_definition.id '_restr_angle.site_symmetry_3'
loop_
_alias.definition_id
'_restr_angle_site_symmetry_3'
_name.category_id restr_angle
_name.object_id site_symmetry_3
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_angle.target
_definition.id '_restr_angle.target'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_angle_target'
_description.text
;
The expectation angle defined by the three atoms.
This is the target angle for the restrained refinement.
;
_name.category_id restr_angle
_name.object_id target
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.range 0:180
_units.code degrees
save_
save_restr_angle.target_weight_param
_definition.id '_restr_angle.target_weight_param'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_angle_target_weight_param'
_description.text
;
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.
;
_name.category_id restr_angle
_name.object_id target_weight_param
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_enumeration.default 0
_enumeration.range 0:180
save_
save_RESTR_DISTANCE
_definition.id RESTR_DISTANCE
_definition.scope Category
_definition.class Loop
_definition.update 2014-06-29
_description.text
;
This category describes restraints applied to
distances during the final refinement.
;
_name.category_id CIF_RSTR
_name.object_id RESTR_DISTANCE
loop_
_category_key.name
'_restr_distance.atom_site_label_1'
'_restr_distance.site_symmetry_1'
'_restr_distance.atom_site_label_2'
'_restr_distance.site_symmetry_2'
save_
save_restr_distance.atom_site_label_1
_definition.id '_restr_distance.atom_site_label_1'
loop_
_alias.definition_id
'_restr_distance_atom_site_label_1'
_name.category_id restr_distance
_name.object_id atom_site_label_1
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_distance.atom_site_label_2
_definition.id '_restr_distance.atom_site_label_2'
loop_
_alias.definition_id
'_restr_distance_atom_site_label_2'
_name.category_id restr_distance
_name.object_id atom_site_label_2
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_distance.details
_definition.id '_restr_distance.details'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_details'
_description.text
;
A free-text description of the restraint.
;
_name.category_id restr_distance
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_restr_distance.diff
_definition.id '_restr_distance.diff'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_diff'
_description.text
;
The difference between the target and the refined distance.
;
_name.category_id restr_distance
_name.object_id diff
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_restr_distance.site_symmetry_1
_definition.id '_restr_distance.site_symmetry_1'
loop_
_alias.definition_id
'_restr_distance_site_symmetry_1'
_name.category_id restr_distance
_name.object_id site_symmetry_1
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_distance.site_symmetry_2
_definition.id '_restr_distance.site_symmetry_2'
loop_
_alias.definition_id
'_restr_distance_site_symmetry_2'
_name.category_id restr_distance
_name.object_id site_symmetry_2
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_distance.target
_definition.id '_restr_distance.target'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_target'
_description.text
;
The expectation distance between the two atoms.
This is the target distance for the restrained refinement.
;
_name.category_id restr_distance
_name.object_id target
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_restr_distance.target_weight_param
_definition.id '_restr_distance.target_weight_param'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_target_weight_param'
_description.text
;
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.
;
_name.category_id restr_distance
_name.object_id target_weight_param
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0
_units.code angstroms
save_
save_RESTR_DISTANCE_MIN
_definition.id RESTR_DISTANCE_MIN
_definition.scope Category
_definition.class Loop
_definition.update 2014-06-29
_description.text
;
Items in this category offer power-law and exponential
expressions for a function designed to prevent two atoms
occupying the same location.
;
_name.category_id CIF_RSTR
_name.object_id RESTR_DISTANCE_MIN
loop_
_category_key.name
'_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'
save_
save_restr_distance_min.A
_definition.id '_restr_distance_min.A'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_A'
_description.text
;
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.
;
_name.category_id restr_distance_min
_name.object_id A
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0
_enumeration.range 0:
save_
save_restr_distance_min.atom_site_label_1
_definition.id '_restr_distance_min.atom_site_label_1'
loop_
_alias.definition_id
'_restr_distance_min_atom_site_label_1'
_name.category_id restr_distance_min
_name.object_id atom_site_label_1
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_distance_min.atom_site_label_2
_definition.id '_restr_distance_min.atom_site_label_2'
loop_
_alias.definition_id
'_restr_distance_min_atom_site_label_2'
_name.category_id restr_distance_min
_name.object_id atom_site_label_2
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_distance_min.B
_definition.id '_restr_distance_min.B'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_B'
_description.text
;
See _restr_distance_min.A for description.
;
_name.category_id restr_distance_min
_name.object_id B
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.default 0
_enumeration.range 0:
_units.code angstroms
save_
save_restr_distance_min.C
_definition.id '_restr_distance_min.C'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_C'
_description.text
;
See _restr_distance_min.A for description.
;
_name.category_id restr_distance_min
_name.object_id C
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
save_
save_restr_distance_min.details
_definition.id '_restr_distance_min.details'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_details'
_description.text
;
A text description of the restraint giving details not
given elsewhere.
;
_name.category_id restr_distance_min
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_restr_distance_min.difference
_definition.id '_restr_distance_min.difference'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_difference'
_description.text
;
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
;
_name.category_id restr_distance_min
_name.object_id difference
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_restr_distance_min.distance
_definition.id '_restr_distance_min.distance'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_distance'
_description.text
;
The refined distance, D, between the two atoms.
;
_name.category_id restr_distance_min
_name.object_id distance
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0:
_units.code angstroms
save_
save_restr_distance_min.E
_definition.id '_restr_distance_min.E'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_E'
_description.text
;
See _restr_distance_min.A for description.
;
_name.category_id restr_distance_min
_name.object_id E
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
save_
save_restr_distance_min.F
_definition.id '_restr_distance_min.F'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_F'
_description.text
;
See _restr_distance_min.A for description.
;
_name.category_id restr_distance_min
_name.object_id F
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_restr_distance_min.G
_definition.id '_restr_distance_min.G'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_distance_min_G'
_description.text
;
See _restr_distance_min.A for description.
;
_name.category_id restr_distance_min
_name.object_id G
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_restr_distance_min.site_symmetry_1
_definition.id '_restr_distance_min.site_symmetry_1'
loop_
_alias.definition_id
'_restr_distance_min_site_symmetry_1'
_name.category_id restr_distance_min
_name.object_id site_symmetry_1
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_distance_min.site_symmetry_2
_definition.id '_restr_distance_min.site_symmetry_2'
loop_
_alias.definition_id
'_restr_distance_min_site_symmetry_2'
_name.category_id restr_distance_min
_name.object_id site_symmetry_2
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_RESTR_EQUAL_ANGLE
_definition.id RESTR_EQUAL_ANGLE
_definition.scope Category
_definition.class Loop
_definition.update 2016-11-15
_description.text
;
Items in this category list the atoms defining the angles
that are restrained to be equal in the final refinement.
_atom_site_label_2 is at the apex of the angle.
;
_name.category_id CIF_RSTR
_name.object_id RESTR_EQUAL_ANGLE
loop_
_category_key.name
'_restr_equal_angle.atom_site_label_1'
'_restr_equal_angle.site_symmetry_1'
'_restr_equal_angle.atom_site_label_2'
'_restr_equal_angle.site_symmetry_2'
'_restr_equal_angle.atom_site_label_3'
'_restr_equal_angle.site_symmetry_3'
save_
save_restr_equal_angle.atom_site_label_1
_definition.id '_restr_equal_angle.atom_site_label_1'
loop_
_alias.definition_id
'_restr_equal_angle_atom_site_label_1'
_name.category_id restr_equal_angle
_name.object_id atom_site_label_1
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_equal_angle.atom_site_label_2
_definition.id '_restr_equal_angle.atom_site_label_2'
loop_
_alias.definition_id
'_restr_equal_angle_atom_site_label_2'
_name.category_id restr_equal_angle
_name.object_id atom_site_label_2
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_equal_angle.atom_site_label_3
_definition.id '_restr_equal_angle.atom_site_label_3'
loop_
_alias.definition_id
'_restr_equal_angle_atom_site_label_3'
_name.category_id restr_equal_angle
_name.object_id atom_site_label_3
_import.get [{'save':restr_label 'file':templ_attr.cif}]
save_
save_restr_equal_angle.class_id
_definition.id '_restr_equal_angle.class_id'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_equal_angle_class_id'
_description.text
;
A character string identifying the class of equal angles
to which this angle belongs.
;
_name.category_id restr_equal_angle
_name.object_id class_id
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Code
save_
save_restr_equal_angle.details
_definition.id '_restr_equal_angle.details'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_equal_angle_details'
_description.text
;
A text description giving details of an angle in
a class of angles that are restrained to be equal.
;
_name.category_id restr_equal_angle
_name.object_id details
_type.purpose Describe
_type.source Recorded
_type.container Single
_type.contents Text
save_
save_restr_equal_angle.site_symmetry_1
_definition.id '_restr_equal_angle.site_symmetry_1'
loop_
_alias.definition_id
'_restr_equal_angle_site_symmetry_1'
_name.category_id restr_equal_angle
_name.object_id site_symmetry_1
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_equal_angle.site_symmetry_2
_definition.id '_restr_equal_angle.site_symmetry_2'
loop_
_alias.definition_id
'_restr_equal_angle_site_symmetry_2'
_name.category_id restr_equal_angle
_name.object_id site_symmetry_2
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_restr_equal_angle.site_symmetry_3
_definition.id '_restr_equal_angle.site_symmetry_3'
loop_
_alias.definition_id
'_restr_equal_angle_site_symmetry_3'
_name.category_id restr_equal_angle
_name.object_id site_symmetry_3
_import.get [{'save':site_symmetry 'file':templ_attr.cif}]
save_
save_RESTR_EQUAL_ANGLE_CLASS
_definition.id RESTR_EQUAL_ANGLE_CLASS
_definition.scope Category
_definition.class Loop
_definition.update 2014-06-29
_description.text
;
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.
;
_name.category_id CIF_RSTR
_name.object_id RESTR_EQUAL_ANGLE_CLASS
_category.key_id '_restr_equal_angle_class.class_id'
loop_
_category_key.name '_restr_equal_angle_class.class_id'
save_
save_restr_equal_angle_class.average
_definition.id '_restr_equal_angle_class.average'
_definition.update 2014-06-29
loop_
_alias.definition_id
'_restr_equal_angle_class_average'
_description.text