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Re: Additional modifications to core CIF for SHELXL2012

Thanks, David.

We could change 'hetero' to something more 
suitable, of course.  Say 'non-carbon atoms' in 
place of hetero in at least the definition text. 
You could also use 'all other atoms' although the 
definition text tends to read more obscurely with 
such wording in the cases where hetero currently 
appears twice in a definition.

Up to you whether or not the 'hetero' part of the 
keyword itself needs changing (some of the 
existing keywords are also obscure until one 
reads the definition).  I daresay my long tenancy 
in an organic institute was peeking through by 
using hetero and even hydrides might be relevant 
here.

But you show by your remarks that even as an 
inorganic expert you did understand what was 
meant.

Cheers,
Tony


>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>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:  <mailto:bm@iucr.org>bm@iucr.org
>>5 Abbey Square, Chester CH1 2HU, England
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>>
>
>
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    University of Zurich
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    Phone:  +41 44 635 4228
    Fax:    +41 44 635 6812

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