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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>, "Spek, A.L. (Ton)" <A.L.Spek@uu.nl>, Tony Linden <alinden@oci.uzh.ch>
- Subject: Re: Additional modifications to core CIF for SHELXL2012
- From: George Sheldrick <gsheldr@shelx.uni-ac.gwdg.de>
- Date: Mon, 05 Nov 2012 16:23:45 +0100
- In-Reply-To: <20121105141457.GA29804@emerald.iucr.org>
- References: <20121105141457.GA29804@emerald.iucr.org>
Dear Brian, Your wording for _reflns_Friedel_fraction_* is fine. I have to draw the line somewhere, otherwise the program can never be released, so on Novermber 1st I drew this line. The suggestions for changing _refine_ls_hydrogen_treatment simply came to my notice too late. It may be my incompetence, but each time I make a change like that I inadvertently introduce at least two new bugs, which requires further testing and further new versions. I will now only fix real bugs before releasing shelxl-2012, otherwise it will no longer be 2012. As I explained in my last email, there would be a good case for deprecating _refine_ls_hydrogen_treatment anyway, because it only repeats information given more specifically by other newer CIF identifiers (and by the embedded .res file). Anyway it needs further discussion, for example I would be in favour of treating NH and OH hydrogens separately rather than putting them in the same basket. Such last-minute fixes often have unintended side-effects, it will just have to wait for the next shelxl release, which will give us adequate time to discuss it. Best wishes, George CC Ton, Tony On 11/05/2012 03:14 PM, 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 > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 _______________________________________________ coreDMG mailing list coreDMG@iucr.org http://mailman.iucr.org/mailman/listinfo/coredmg
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