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Re: Draft changes to Core data names for multiplicity etc.
- To: Brian McMahon <firstname.lastname@example.org>, email@example.com
- Subject: Re: Draft changes to Core data names for multiplicity etc.
- From: "Herbert J. Bernstein" <firstname.lastname@example.org>
- Date: Wed, 16 May 2012 11:07:19 -0400
- In-Reply-To: <20120516103234.GA13856@emerald.iucr.org>
- References: <20120516103234.GA13856@emerald.iucr.org>
I am not sure if I am "in" or just a kibbitzer. but this sounds sensible to me. -- Herbert On 5/16/12 6:32 AM, Brian McMahon wrote: > 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 > > _______________________________________________ coreDMG mailing list coreDMG@iucr.org http://mailman.iucr.org/mailman/listinfo/coredmg
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