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Draft changes to Core data names for multiplicity etc.
- To: email@example.com
- Subject: Draft changes to Core data names for multiplicity etc.
- From: Brian McMahon <firstname.lastname@example.org>
- 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@example.com 5 Abbey Square, Chester CH1 2HU, England _______________________________________________ coreDMG mailing list coreDMG@iucr.org http://mailman.iucr.org/mailman/listinfo/coredmg
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- Re: Draft changes to Core data names for multiplicity etc. (George Sheldrick)
- Re: Draft changes to Core data names for multiplicity etc. (Howard Flack)
- Re: Draft changes to Core data names for multiplicity etc. (Herbert J. Bernstein)
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