Discussion List Archives

[Date Prev][Date Next][Date Index]

(51) Fine tuning of CIF Core version 2.0

  • To: COMCIFS@iucr.ac.uk
  • Subject: (51) Fine tuning of CIF Core version 2.0
  • From: bm
  • Date: Tue, 12 Nov 1996 13:04:09 GMT
Dear Colleagues

Thank you for your approval for the Core dictionary and for the many helpful
comments that I've recently received. As a result of these, some small
changes have been made; these are summarised below.

I draw your attention in particular to the following changes of substance:

The enumeration range for _atom_site_attached_hydrogens has been extended
from 0:4 to 0:8 after Paul Edgington found some examples with values up to
8 in the Cambridge Database. Thanks, Paul.

The entry 'constr' meaning 'H parameters constrained' has been added to
_refine_ls_hydrogen_treatment to indicate that constraints were applied
(typically riding-model constraints) to the H-atom refinement. Note that this
data name is intended to summarise the overall approach to the treatment of
H atoms; individual atoms can be described in more detail using
_atom_site_refinement_flags.

The enumeration range for _diffrn_standards_decay_% has been changed to
":100" to permit the recording of experimentally observed negative decays,
and also to constrain the total decay to be no more than 100%.

There is still some active discussion with the mmCIF group on the proper
treatment of the various diffrn categories to permit a complete description
of multiple experiments and associated data sets contributing to the raw
data collected in the course of a structure determination.  It is likely
that version 2.0 of the core will NOT contain the facility to describe
multiple data sets; but a consistent set of data names that may be looped to
describe different data sets will be supplied for the next version, 2.1 of
the core, which may well accompany the release of mmCIF version 1.0. In
other words, the changes needed to accommodate multiple data sets are
not great, but are not yet completely agreed for this release. This
has some bearing also on the considerations for describing area detectors
that Syd and David are tackling, with reference to Andy Hammersley's
comments on the requirements for automatic handling of experimental
operating parameters. 

The one major change arising from this debate is the desire to delete
_diffrn_radiation_detector and *_source from this version of the core. These
are published data names, and I propose to make them available to future
applications by adding them to the cif_compat.dic that also holds the
now deprecated _cell_length_a_nm and other units-dependent data names.

I hope to be able to declare version 2.0 complete and on release in the next
few days.

Regards
Brian

----------------------------------------------------------------------------
   1996-10-15  BMcM:
               Modified description of example for DIFFRN_REFLN
               Changed _enumeration_range of atom_site_attached_hydrogens
                 from 0:4 to 0:8 (cf CSD entry with refcode DUTMAG01) (PRE)
               Added '_enumeration_default cif' to _publ_body_format
               Changed underscores to spaces in the example for the Hall
                 spacegroup symbol in data_symmetry_[]
               Deleted extraneous '_' in data_(_)citation_abstract_id_CAS
   1996-10-27  BMcM: Changed psiscan to psi-scan at request of SRH
   1996-11-05  BMcM:
               Changed _citation_book_coden_ISBN to _citation_book_id_ISBN,
                 _citation_journal_coden_ASTM to _citation_journal_id_ASTM,
                 _citation_journal_coden_CSD to _citation_journal_id_CSD,
                 _citation_journal_coden_ISSN to _citation_journal_id_ISSN,
                 and _citation_Medline_AN to _citation_database_id_Medline.
                 Also modified description of CODEN in _citation_journal_id_ASTM
                 and _database_journal_ASTM (suggested by PMDF)
               The phrase 'diffraction data' modified to 'intensities' in
                 several places, some other cosmetic commas and enforcement
                 of consistent lower-case units names (PMDF)
               Clarification of the definition for
                 _diffrn_radiation_polarisn_norm (PMDF)
               Added 'constr' to _refine_ls_hydrogen_treatment (SRH)
               Corrected misassignment of category of
                 _diffrn_radiation_detector_dtime (H.J.Bernstein)
   1996-11-06  BMcM:
               Added "_list   yes" to items in the REFLNS_SHELL category (IDB)
               Added "measured" to definition of _reflns_shell_number_unique_all
               Changed enumeration range for _diffrn_standards_decay_% to
                 ":100" and added statement about negative values (PMDF/SRH)
   1996-11-08  BMcM:
               _diffrn_radiation_detector, _diffrn_radiation_detector_dtime and
                 _diffrn_radiation_source removed (these will be transferred to
                 cif_compat.dic for compatibility with files conforming to the
                 original dictionary)
               _diffrn_radiation_wavelength_* items moved to new category
   1996-11-12  BMcM:
               Deleted _cell_id and _cell_measurement_reflns_id, and
                 clarified the intent of the CELL category in _cell_[]
               Some small rewordings of various _diffrn_* items due to
                 B.H.Toby
----------------------------------------------------------------------------