Addendum to CIF restraints and constraints
David Brown
idbrown at mcmaster.ca
Mon Apr 19 15:30:22 BST 2010
Dear Colleagues in the CIF Core Diotionary Maintenance Group (and others)
In January I circulated to the CIF core Dictionary Maintenance Group a
proposal that would allow authors to describe the restraints and
constraints that were applied during a structure refinement. A .txt
version of that document is attached in case you wish to refer to it.
It was put together by Ilia Guzei and myself and contains, inter alia, a
description of the philosphy that we adopted in drawing up the
document. Briefly, this points out the the information is for reporting
a restraint or constraint in a simple crystallographic format and is not
intended to reflect the methods used in the refinement to implement the
restraint since these can be quite varied.
There were a small number of responses to the document and after giving
these careful consideration we have decided not to make any changes to
the original document other than adding two more restraints, one in
which the atomic displacement parameters of an atom are restrained to be
isotropic, and the other where they are restrained to be similar to
another specified atom. The dictionary code for these new items are
appended below at the end of this email.
THESE TWO DOCUMENTS ARE NOW OPEN FOR DISCUSSION AND WILL REMAIN SO FOR
THE NEXT SIX WEEKS. If there are no unresolved issues by 2010-05-31
(end of May) the attached and appended documents will be combined and
submitted to COMCIFS for final approval.
David Brown
----------------------- APPENDED FILE ---------------------------
# 2010-04-19
# Addendum to the proposed addition of restraint and constraint descriptors
# circulated 2010-01-13
#
# These two additional restraints allow anisotropic atomic displacement
parameters
# to be restrainted to isotropic (SHLEX ISO), and the anisotropic atomic
# displacement parameters of one atom to be restrained to be similar to
those of
# another specified atom (SHELX SIMU)
#
# As before, setting the weighting parameter to zero changes the
restraint into a
# constraint.
#####################
# #
# 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.
;
#####################
# #
# 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 additions to proposed Restraint and Constraint Dictionary
----------##
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