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enumeration values

  • Subject: enumeration values
  • From: Richard Gildea <rgildea@xxxxxxxxx>
  • Date: Fri, 4 Jun 2010 19:42:34 +0100
  • In-Reply-To: <AANLkTil-uCJIT-Rg_07zc3FTtY3ln8FMiOvAhcsGWAPq@mail.gmail.com>
  • References: <AANLkTil-uCJIT-Rg_07zc3FTtY3ln8FMiOvAhcsGWAPq@mail.gmail.com>
Dear All,

The enumeration entry in cif_core.dic for _atom_site_refinement_flags is as follows:

loop_ _enumeration
_enumeration_detail . 'no refinement constraints'
                               S 'special-position constraint on site'
                               G 'rigid-group refinement of site'
                               R 'riding-atom site attached to non-riding atom'
                               D 'distance or angle restraint on site'
                               T 'thermal displacement constraints'
                               U 'Uiso or Uij restraint (rigid bond)'
                               P 'partial occupancy constraint'

No combinations are specified explicitly as being allowed, which is in contrast to the entry for _atom_site_refinement_flags_posn:

loop_ _enumeration
                     . 'no constraints on  positional coordinates'
                     D 'distance or angle restraint on positional coordinates'
                     G 'rigid-group refinement of positional coordinates'
                     R 'riding-atom site attached to non-riding atom'
                     S 'special-position constraint on positional coordinates'
                     DG   'combination of the above constraints'
                     DR   'combination of the above constraints'
                     DS   'combination of the above constraints'
                     GR   'combination of the above constraints'
                     GS   'combination of the above constraints'
                     RS    'combination of the above constraints'
                     DGR  'combination of the above constraints'
                     DGS  'combination of the above constraints'
                     DRS  'combination of the above constraints'
                     GRS  'combination of the above constraints'
                     DGRS 'combination of the above constraints'

The text of the definition for _atom_site_refinement_flags refers to a "concatenated series of single-letter codes", which suggests that combinations of the code are allowed.  This is in contrast to the text at the html version of the dictionary (http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_refinement_flags.html) which states (a little ambiguously) "The data value must be ONE of the following:" (my emphasis), before the list of single letter codes.

Is it an oversight that the allowed combinations are missing from the enumeration list for _atom_site_refinement_flags? As it is, a program validating against the cif_core.dic would (I suspect incorrectly) flag a value of, for example, 'PR' as an invalid value for the item _atom_site_refinement_flags.  PyCifRW is one such program that flags these concatenated values as being outside the permitted set. Without the allowed combinations being also included in the list, it makes it hard to programmatically validate such combinations.  Alternatively, if combinations are not allowed, then this would render many files as output by SHELXL to be invalid (for example when a hydrogen is riding on a partially occupied atom).

I have a further question about case sensitivity of data values.  The cif specification states that the case of data values must be respected - does this mean therefore that, for example, a value of 'Monoclinic' for _symmetry_cell_setting (a commonly encountered case, judging by our local database of CIFs) should be flagged as being outside of the permitted set, or should it be allowed as valid?



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