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Re: New version (2.3) of core CIF dictionary available



On Mon, 6 Oct 2003, Howard Flack wrote:

> _geom_angle_site_symmetry
>
>    question:  Does the publication  Hall, S. R. (1981). Acta Cryst. A37,
> 517-525 specify and guarantee a unique "equivalent position code 'n'"
> for each and every symmetry operation in the space group (i.e. the
> infinite number of operations)

No.  There is, as I recall, nothing in this publication about the ordering
of the symmetry operations.  The equivalent position code is required by
CIF for internal reference but has nothing to do with the Hall symbol
itself, nor with any of the other symbols that appear in International
Tables which itself does not claim to produce an ordered or labelled list
of symmetry operations.  There are clearly many different orders in which
the equivalent positions (or symmetry operations) can be generated from
the Hall symbol.  The equivalent position number will depend on the
particular software used.

In the first versions of CIF there was no item for
_symmetry_equivalent_posn_site_id and the equivalent position number in
the GEOM_* categories referred to the position of the relevant symmetry
operation in the ordered SYMMETRY_EQUIV list, hence the use of the word
'number' rather than 'code'.  This violated the CIF rules which require
that items may appear in any order in a CIF, i.e., shuffling the list of
symmetry operations should not invalidate the CIF, but clearly would
unless each symmetry operation was accompanied by its own identifier.  It
was for this reason that we added _*_id, specifying that it should be a
number.  We did not, at the time, see that it was necessary to update the
wording in the geom sections.

With the replacement of the SYMMETRY_EQUIV category with SPACE_GROUP_SYMOP
we have replaced _symmetry_equivalent_posn_site_id with
_space_group_symop_id and the wording in the GEOM_* categories should be
changed to reflect this.  There is one problem, the new _*_id is defined
as 'char' which opens up the possibility that symmetry codes in GEOM_* may
contain characters other than numbers.  As you suggest, the Core
Dictionary Maintenance Group (DMG) needs to take the symmetry definitions
in GEOM_* under advisement.  Since the geom symmetry code was first
defined, CIF has moved several steps away from having parsable data values
and the answer may be to separate out the different components which would
also have the advantage of allowing the links between SPACE_GROUP_SYMOP
and GEOM_* to be made explicit in the dictionary.  We should continue this
discussion in the Core DMG whose discussions are open to public view on
the IUCr web site.  I will add it to the coreDMG agenda.

		Thanks for pointing out the inconsistency,

				David




*****************************************************
Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773
idbrown@mcmaster.ca
*****************************************************



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