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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


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