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Draft changes to Core data names for multiplicity etc.
- To: [email protected]
- Subject: Draft changes to Core data names for multiplicity etc.
- From: Brian McMahon <[email protected]>
- Date: Wed, 16 May 2012 11:32:34 +0100
Dear Colleagues
This message is being sent to members of the CIF Core Dictionary
Management Group, who are requested to respond to it at your
earliest convenience. A copy will also be sent to other software
developers for their early information.
Some programs have output values for the core data item
_atom_site_symmetry_multiplicity that are actually the order
of the space-group site symmetry and not the multiplicity as
defined in International Tables. As a result, the values given
in CIFs in the IUCr archive and elsewhere are ambiguous.
It is proposed to remove this ambiguity by deprecating the
existing data name _atom_site_symmetry_multiplicity and replacing it
with two new names,
_atom_site_site_symmetry_multiplicity
_atom_site_site_symmetry_order
formal definitions of which are given below.
This will allow future "remediation" of the IUCr CIF archive to
remove this ambiguity; and software authors may cleanly update their
output in the next release cycle of their programs. In practice,
we think that the usage of existing CIFs will not be greatly affected,
since most programs do not import and use the site multiplicities
directly; but by making this formal change we will also be drawing
attention to the need for end-users who do rely on this value to
validate it before use.
Please let us know whether you agree to, or have any objections to
this approach, as soon as possible.
For your information, it is proposed also to make two small editorial
changes to other data items (clarifying that F(000) may be given
in the case of neutron diffraction experiments, and sanctioning the
use of standard uncertainties when quoting the wavelength, as is
practice in powder diffraction). The details are also included below.
Best wishes
Brian McMahon
COMCIFS Coordinating Secretary
-------------------------------------------------------------------
_dictionary_history
;
(extract)
2012-05-15 BMcM: Deprecated _atom_site_symmetry_multiplicity;
replaced with _atom_site_site_symmetry_multiplicity
and added _atom_site_site_symmetry_order (IDB)
Reworded _exptl_crystal_F_000 definition to take
account of neutron diffraction and removed
_enumeration_range (can be negative for neutrons)
Added '_type_conditions su' to _diffrn_radiation_wavelength
;
data_atom_site_symmetry_multiplicity
_name '_atom_site_symmetry_multiplicity'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_site_symmetry_multiplicity'
_related_function replace
_enumeration_range 1:192
_definition
; The multiplicity of a site due to the space-group symmetry as
given in International Tables for Crystallography Vol. A (2002).
Use of this data name is deprecated because of
inconsistencies in practice among structure refinement
software packages. The number of positions given for
this Wyckoff site in International Tables for
Crystallography Vol. A (2002). should now be expressed
using the data name _atom_site_site_symmetry_multiplicity.
In the historic archive some CIFs use this item to give values
that belong in _atom_site_site_symmetry_order.
;
data_atom_site_site_symmetry_multiplicity
_name '_atom_site_site_symmetry_multiplicity'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_symmetry_multiplicity'
_related_function alternate
_enumeration_range 1:192
_definition
; The number of different sites that are generated by the
application of the space-group symmetry to the
coordinates given for this site. It is equal to the
multiplicity given for this Wyckoff site
in International Tables for Crystallography Vol. A (2002).
It is equal to the multiplicity of the general position
divided by the order of the site symmetry given in
_atom_site_site_symmetry_order.
;
data_atom_site_site_symmetry_order
_name '_atom_site_site_symmetry_order'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_enumeration_range 1:48
_definition
; The order of the site symmetry of the site identified by
_atom_site_label.
This is the number of times application of the
crystallographic symmetry to the coordinates given for
this site generates the same set of coordinates.
It is equal to:
multiplicity of the general position
------------------------------------
multiplicity of this site
where 'multiplicity of this site' is
given in _atom_site_site_symmetry_multiplicity.
;
data_diffrn_radiation_wavelength
_name '_diffrn_radiation_wavelength'
_category diffrn_radiation_wavelength
_type numb
_type_conditions su
_list both
_list_reference '_diffrn_radiation_wavelength_id'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The radiation wavelength in angstroms.
;
data_exptl_crystal_F_000
_name '_exptl_crystal_F_000'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_definition
; The expression for a structure factor evaluated in the
zeroth-order case h = k = l = 0, F(000). This may contain
dispersion contributions and is calculated as
F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^
f~r~ = real part of the scattering factors at theta = 0
f~i~ = imaginary part of the scattering factors at theta = 0
the sum is taken over each atom in the unit cell
For X-rays, non-dispersive F(000) is a positive number
and counts the effective number of electrons in the unit cell;
for neutrons, non-dispersive F(000) (which may be negative)
counts the total nuclear scattering power in the unit cell. See
http://reference.iucr.org/dictionary/F(000)
;
------------------------------------------------------------------------------
Brian McMahon tel: +44 1244 342878
Research and Development Officer fax: +44 1244 314888
International Union of Crystallography e-mail: [email protected]
5 Abbey Square, Chester CH1 2HU, England
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