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Re: Additional modifications to core CIF for SHELXL2012

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
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begin:vcard
fn:I.David Brown
n:Brown;I.David
org:McMaster University;Brockhouse Institute for Materials Research
adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada
email;internet:idbrown@mcmaster.ca
title:Professor Emeritus
tel;work:+905 525 9140 x 24710
tel;fax:+905 521 2773
version:2.1
end:vcard

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