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Re: Additional modifications to core CIF for SHELXL2012
- To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
- Subject: Re: Additional modifications to core CIF for SHELXL2012
- From: David Brown <idbrown@mcmaster.ca>
- Date: Wed, 07 Nov 2012 09:55:42 -0500
- In-Reply-To: <20121105141457.GA29804@emerald.iucr.org>
- References: <20121105141457.GA29804@emerald.iucr.org>
My only comment on Brian's proposal is to ask for a clear
definition of 'heteroatom'. As an inorganic crystallographer I do
not deal in heteroatoms and so would be unsure which of the
various comments to use. It is an expression that has no meaning
outside of organic chemistry though a hetero label could well be
relevant in a tetramethyl ammonium or a methyl sulfonate salt. I
suspect that 'hetero' means any atom other than carbon. Would it
be clearer to say 'non-carbon atoms', or even 'other atoms' since
all the proposed 'hetero' label start with 'constrained refinement
of H on C' and there would be no ambiguity in using 'other'. David Brown On 11/5/2012 9:14 AM, Brian McMahon wrote: Now that SHELXL2012 is nearing final release, we should formally publish the version of the core dictionary that incorporates the changes discussed earlier on this list (see the thread starting at http://www.iucr.org/__data/iucr/lists/coredmg/msg00286.html) There are two points I would like to raise, for which an early response would be a great help. (1) My latest draft includes definitions for George Sheldrick's requested _reflns_Friedel_fraction_full and *_max (see Annex 1 below). Please check that my slight rewording of George's definition (so that each item can have a standalone definition) is correct. (2) Tony Linden wishes to add some further information to _refine_ls_hydrogen_treatment in order to make it clearer in synoptic form to journal reviewers what the H-atom treatment strategy was. It's acknowledged that no finite list of labels will accommodate all possible strategies, but he suggests that the extended list (in Annex 2 below) will cover a large proportion of existing strategies that currently reside in undifferentiated form under the 'mixed' designation. Please comment on whether you think this is a reasonable strategy. Regards Brian ------------------------------------------------------------------------------ Annex 1: New definitions for _reflns_Friedel_fraction_* data_reflns_Friedel_fraction_full _name '_reflns_Friedel_fraction_full' _category reflns _type numb _enumeration_range 0.0:1.0 _definition ; The number of Friedel pairs measured out to _diffrn_reflns_theta_full. divided by the number theoretically possible (ignoring reflections in centric projections and systematic absences throughout). In contrast to _reflns_Friedel_coverage this can take values in the full range 0 to 1 for any non-centrosymmetric space group, and so one can see at a glance how completely the Friedel pairs have been measured. For centrosymmetric space groups the value would be 0/0 and so would be given as '.'. ; data_reflns_Friedel_fraction_max _name '_reflns_Friedel_fraction_max' _category reflns _type numb _enumeration_range 0.0:1.0 _definition ; The number of Friedel pairs measured out to _diffrn_reflns_theta_max. divided by the number theoretically possible (ignoring reflections in centric projections and systematic absences throughout). In contrast to _reflns_Friedel_coverage this can take values in the full range 0 to 1 for any non-centrosymmetric space group, and so one can see at a glance how completely the Friedel pairs have been measured. For centrosymmetric space groups the value would be 0/0 and so would be given as '.'. ; ------------------------------------------------------------------------------ ANNEX 2: New enumeration values for _refine_ls_hydrogen_treatment (all those enumeration values with "hetero" are new): data_refine_ls_hydrogen_treatment _name '_refine_ls_hydrogen_treatment' _category refine _type char loop_ _enumeration _enumeration_detail refall 'refined all H-atom parameters' refxyz 'refined H-atom coordinates only' refU 'refined H-atom U's only' noref 'no refinement of H-atom parameters' constr 'H-atom parameters constrained' hetero ; H-atom parameters constrained for H on C, all H-atom parameters refined for H on heteroatoms ; heteroxyz ; H-atom parameters constrained for H on C, refined H-atom coordinates only for H on heteroatoms ; heteroU ; H-atom parameters constrained for H on C, refined H-atom U's only for H on heteroatoms ; heteronoref ; H-atom parameters constrained for H on C, no refinement of H-atom parameters for H on heteroatoms ; hetero-mixed ; H-atom parameters constrained for H on C and some heteroatoms, all H-atom parameters refined for H on remaining heteroatoms ; heteroxyz-mixed ; H-atom parameters constrained for H on C and some heteroatoms, refined H-atom coordinates only for H on remaining heteroatoms ; heteroU-mixed ; H-atom parameters constrained for H on C and some heteroatoms, refined H-atom U's only for H on remaining heteroatoms ; heteronoref-mixed ; H-atom parameters constrained for H on C and some heteroatoms, no refinement of H-atom parameters for H on remaining heteroatoms ; mixed 'some constrained, some independent' undef 'H-atom parameters not defined' _enumeration_default undef _definition ; Treatment of hydrogen atoms in the least-squares refinement. ; ------------------------------------------------------------------------------ _________________________________________________________________________ Brian McMahon tel: +44 1244 342878 Research and Development Officer fax: +44 1244 314888 International Union of Crystallography e-mail: bm@iucr.org 5 Abbey Square, Chester CH1 2HU, England _______________________________________________ coreDMG mailing list coreDMG@iucr.org http://mailman.iucr.org/mailman/listinfo/coredmg |
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