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Core restraints dictionary v 0.0.3 for COMCIFS approval
- To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
- Subject: Core restraints dictionary v 0.0.3 for COMCIFS approval
- From: James Hester <jamesrhester@gmail.com>
- Date: Tue, 21 Sep 2010 22:14:27 +1000
Dear COMCIFS,
Following this email is a new version of the restraints dictionary,
which has been revised according to Herbert's suggestion and has now
once again been submitted to COMCIFS for final approval. The
dictionary will be considered approved once all voting members have
voted to approve it, or else no objections have been received in the
next 6 weeks, whichever occurs first.
James.
=======================================
##############################################################################
# #
# CIF RESTRAINTS AND CONSTRAINTS DICTIONARY VERSION 0.03 #
# ------------------------------------------------------ #
# #
# Proposed dictionary code for reporting restraints and constraints in the #
# core CIF dictionary #
# #
# This dictionary contains the names and definitions proposed for reporting #
# restraints and constraints in the Core CIF dictionary #
# #
# 2010-09-15 #
# This dictionary has been approved by the core dictionary maintenance group #
# The items described below have been preseneted for final approvcal by #
# COMCIFS on behalf of the International Union of Crystallography #
# #
# Copyright 2010 International Union of Crystallography #
##############################################################################
##############################################################################
# #
# Some notes on the philosophy followed in this dictionary #
# -------------------------------------------------------- #
# 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 0.3
_dictionary_update 2010-09-15
_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 reveiw
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
2010-10-15 IDB: The revised rigid body description is added.
;
#
# 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 categroy_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 descring 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
_definition
; Items in this category define angles that were restrained in the final
refinement.
;
_example
; 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 ?
;
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_'
_units degrees
_enumeration_range 0:
_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_'
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 three atoms that define the angle.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_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 +
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_'
_units degrees
_enumeration_range 0:180
_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_'
_units degrees
_enumeration_range 0:180
_enumeration_default 0
_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
; Category of items that describes restraints applied to distances
during the final refinement.
;
_example
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
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 ?
;
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 to be 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
_list yes
_list_reference '_restr_distance_atom_site_label_'
_type_conditions su
_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 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 a symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It should 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_'
_units A
_units_detail Angstrom
_enumeration_default 0
_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.
;
_example
;
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'
;
data_restr_distance_min_A
_name '_restr_distance_min_A'
_category 'restr_distance_min'
_type numb
_list yes
_list_reference 'restr_distance_min_atomi_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
; _atom_site_labels for the two atoms that are to be 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_atomi_site_label_'
_units A
_units_detail Angstrom
_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_C
_name '_restr_distance_min_C'
_category 'restr_distance_min'
_type numb
_list yes
_list_reference 'restr_distance_min_atomi_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_detail'
_category 'restr_distance_min'
_type char
_list yes
_list_reference 'restr_distance_min_atomi_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_atomi_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_atomi_site_label_'
_units A
_units_detail Angstrom
_enumeration_range 0:
_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_atomi_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_atomi_site_label_'
_units A
_units_detail Angstrom
_enumeration_range 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_G
_name '_restr_distance_min_G'
_category 'restr_distance_min'
_type numb
_list yes
_list_reference 'restr_distance_min_atomi_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_atomi_site_label_'
_definition
; The site symmetries of the two atoms to be kept apart.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry-transformed coordinates to generate
the atom that are to be 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 to be 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.
;
_example
;
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_details
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 ?
;
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 to be 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_details'
_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_label_
loop_ _name '_restr_equal_angle_site_symmetry_label_1'
'_restr_equal_angle_site_symmetry_label_2'
'_restr_equal_angle_site_symmetry_label_3'
_category 'restr_equal_angle'
_type char
_list yes
_list_reference '_restr_equal_angle_atom_site_label_'
_definition
; The site symmetries of the three atoms that define an angle
to be restrained to be equal to other angles in the same class.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_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.
;
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
###################################
# #
# 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.
;
_example
;
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_details
1 0.50 123.52 0.32 0.62 ?
2 0.50 118.23 0.52 1.43 ?
;
data_restr_equal_angle_class_average
_name '_restr_equal_angle_class_average'
_category 'restr_equal_angle_class'
_type numb
_list yes
_units degrees
_enumeration_range 0:
_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_details
_name '_restr_equal_angle_class_details'
_category 'restr_equal_angle_class'
_type char
_list yes
_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
_units degrees
_enumeration_range 0:
_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
_units degrees
_enumeration_range 0:
_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
_units degrees
_enumeration_range 0:
_enumeration_default 0
_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 to be 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.
;
_example
;
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 ?
;
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 to be 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_label_
loop_ _name '_restr_equal_distance_site_symmetry_label_1'
'_restr_equal_distance_site_symmetry_label_2'
_category 'restr_equal_distance'
_type char
_list yes
_list_reference '_restr_equal_distance_atom_site_label_'
_definition
; The site symmetries of the two atoms that define a distance
to be restrained to be equal to other distances in the same class.
The symmetry code of each atom site 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 should a number given in
_space_group_symop_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.
;
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
###################################
# #
# 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.
;
_example
;
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 ?
;
data_restr_equal_distance_class_average
_name '_restr_equal_distance_class_average'
_category 'restr_equal_distance_class'
_type numb
_list yes
_units A
_units_detail Angstrom
_enumeration_range 0:
_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
_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
_units A
_units_detail Angstrom
_enumeration_range 0:
_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 yes
_units Angstrom
_enumeration_range 0:
_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
_units A
_units_detail Angstrom
_enumeration_range 0:
_enumeration_default 0
_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 to be 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.
;
_example
;
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 ?
;
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 to be 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
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_label_
loop_ _name '_restr_equal_torsion_site_symmetry_label_1'
'_restr_equal_torsion_site_symmetry_label_2'
'_restr_equal_torsion_site_symmetry_label_3'
'_restr_equal_torsion_site_symmetry_label_4'
_category 'restr_equal_torsion'
_type char
_list yes
_list_reference '_restr_equal_torsion_atom_site_label_'
_enumeration_default 1_555
_definition
; The site symmetries of the four atoms that define a torsion angle
to be restrained to be equal to other torsion angles in the
same class.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_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.
;
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'
###################################
# #
# 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
nagles for each class of torsion angles that are restrained
to be equal in the final refinement.
;
_example
;
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 ?
;
data_restr_equal_torsion_class_average
_name '_restr_equal_torsion_class_average'
_category 'restr_equal_torsion_class'
_type numb
_list yes
_units degrees
_enumeration_range 0:
_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
_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
_units degrees
_enumeration_range 0:
_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
_units degrees
_enumeration_range 0:
_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
_units degrees
_enumeration_range 0:
_enumeration_default 0
_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
_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.
;
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 loop restr_parameter_class.
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
;
;
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
;
;
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
;
; 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
;
;
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)
;
# ---------------------------- end of examples -------------------
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 qantity being restrained.
It can be used to convert a constraint on occupance 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
_list_reference '_restr_parameter_class_class_id'
_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.
;
_example
# ------------------------------------------------------
;
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_detail
; 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_coeffcient 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
;
# --------------------------------------------------------------
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 and 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
_definition
; Items in this category define the atoms that make up each class of plane.
;
_example
;
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) ?
;
data_restr_plane_atom_site_label
_name '_restr_plane_atom_site_label'
_category 'restr_plane'
_type char
_list yes
_list_reference ?
_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_reference ?
_list_mandatory yes
_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 ?
_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 ?
_units A
_units_details Angstrom
_enumeration_range 0:
_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_reference ?
_list_mandatory yes
_enumeration_default '1_555'
_definition
; The site symmetries of the atom that helps to define the plane
to which it to be restrained.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_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.
;
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_plane_target_weight_param
_name '_restr_plane_target_weight_param'
_category 'restr_plane'
_type numb
_list yes
_units A
_units_detail Angstrom
_enumeration_range 0:
_enumeration_default 0.
_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 thiscategory describe the properties of
the different groups of atoms that are restrained
to form a plain.
;
_example
;
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
_resrt_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'
;
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'
_units A
_units_detail Angstrom
_enumeration_range 0:
_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'
_units A
_units_detail Angstrom
_enumeration_range 0:
_definition
; The distance in Angstrom 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'
_definition
; The site symmetries of the atom that helps to define the plane
to which it to be restrained.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_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.
;
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'
#
#--------------------------------------------------------------
# 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
_definition
; Items in this category list the atoms defining the one or
more bodies that are constrained to be rigid in the final
refinement. This is done by listing the atom_site_label
and symop 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.
;
loop_ _example _example_details
;
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 ?
;
; The first rigid body contains C1, C2, C3 and C4, the second rigid body
contains C3, C4, C5 and C6. The boond beteeen C3 and C4 is common to both
rigid bodies
;
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
;
_example ?
_example_detail ?
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_label_
_name '_restr_rigid_body_site_symmetry'
_category 'restr_rigid_body'
_type char
_list yes
_list_reference '_restr_rigid_body_id'
_definition
; The site symmetry of an atom in a rigid body
The symmetry code of each atom site 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 should the number given in
_space_group_symop_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.
;
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
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 distance in
a class of distances 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
_definition
; Items in this category give details of the dfferent rigid
bodies as defined by _restr_rigid_body_class_id
;
_example
;
loop_
_restr_rigid_body_class_class_id
_restr_rigid_body_class_details
1 'Phenyl ring'
2 'methyl group'
;
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
_definition
; Items in this category define torsion angles that were restrained
in the final refinement.
;
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
_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 ?
;
; An example of a torsion angle restrained to 90+/-1 degree with a refined
difference of 0.97 degrees.
;
data_restr_torsion_angle_target
_name '_restr_torsion_angle_target'
_category 'restr_torsion'
_type numb
_list yes
_list_reference '_restr_torsion_atom_site_label_'
_units degree
_enumeration_range -180:180
_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_'
_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 four atoms that define the torsion angle.
The symmetry code of each atom site 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 should match a number given in
_space_group_symop_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_'
_units degree
_enumeration_range 0:
_enumeration_default 0
_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 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'
_definition
; This restraints attempts to make an anisotropic
atomic displaecement isotropic within the range of the
weighting parameter.
It corresponds to SHELX ISO.
;
loop_
_example
;loop_
_restr_U_iso_atom_site_label
_restr_U_iso_weight_param
Na1 0.003
O3 0.008
O8 0.008
;
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 to be restrained.
;
data_restr_U_isotropic_weight_param
_name '_restr_U_iso_weight_param'
_category 'restr_U_iso'
_type numb
_list yes
_list_reference '_restr_U_iso_atom_site_label'
_units A^-2^
_units_detail 'reciprocal Angstrom squared'
_enumeration_range 0:
_enumeration_default 0
_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
_definition
; The items in this category restrains the anisotropic displacement
parameters of two atoms to be equal within a certain
_weight_param along the direction of the vector joining the atoms.
;
_example
;
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'
;
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 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 should match a number given in
_space_group_symop_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_'
_units A^-2^
_units_detail Angstrom^-2^
_enumeration_default 0
_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 as 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_'
_units A^-2^
_units_detail Angstrom^-2^
_enumeration_default 0
_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 RESRAINED TO HAVE THE SAME ADPs
#--------------------------------------------------------------------
#
#####################
# #
# RESTR_U-SIMILAR #
# #
#####################
data_restr_U_similar_[]
_name '_restr_U_similar_[]'
_category category_overview
_type null
_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
;
loop_
_example
;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
;
data_restr_U_similar_atom_site_label_1
_name '_restr_U_similar_atom_site_label_1'
_category 'restr_U_similar'
_type char
_list yes
loop_
_list_reference '_restr_U_similar_atom_site_label_1'
'_restr_U_similar_atom_site_label_2'
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; Atom site label of first atom, the atom whose
atomic displacement parameters are used as the target.
;
data_restr_U_similar_atom_site_label_2
_name '_restr_U_similar_atom_site_label_2'
_category 'restr_U_similar'
_type char
_list yes
loop_
_list_reference '_restr_U_similar_atom_site_label_1'
'_restr_U_similar_atom_site_label_2'
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; Atom site label of second atom, the atom whose
atomic displacement parameters are to be restrained
to be the same at atom 1.
;
data_restr_U_similar_weight_param
_name '_restr_U_similar_weight_param'
_category 'restr_U_similar'
_type numb
_list yes
loop_
_list_reference '_restr_U_similar_atom_site_label_1'
'_restr_U_similar_atom_site_label_2'
_units A^-2^
_units_detail 'reciprocal Angstrom squared'
_enumeration_range 0:
_enumeration_default 0
_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 ---------
--
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