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

Re: CIF: Getting a structure drawing program to create a

• Subject: Re: CIF: Getting a structure drawing program to create a
• From: louis@xxxxxxxxxxxxxx
• Date: Thu, 21 Dec 2000 08:28:14 GMT

Dear Lachlan

The "high quality" CIF importer in WinGX uses the CIFtbx API library of
Hall & Bernstein. This requires that the CIF should conform to the standard
syntax outlined in the public domain documentation from the IUCr site. Any
CIF which
fails to meet these (rather simple) requirements will fail to be succesfully
imported.
However this is merely the first hurdle. The CIF standard makes NO demands
on the
actual information present in a CIF, which is one reason that importing programs
can have dificulties making sense of the file. A CIF containing merely a
data_ statement
would be a legal CIF, but clearly an inadequate one !

The WinGX importer is basically my original 
CIF2SX program, ie. it is trying to create a SHELX file and needs to know
some basic information
about the unit cell dimensions, cell errors, cell contents,wavelength, Z,
space group, atom types, 
coordinates and thermal parameters (geometric information is derivative and
unnecessary).
CIF's may  contain  redundant information, e.g. _symmetry_space_group_name_H-M
and      _symmetry_equiv_pos_as_xyz  Either one is (often) enough to define
a space group, though
the Hall symbol is  to be preferred to the HM symbol as it is less ambiguous.
Generally the most serious problem is in getting the atomic types. You would
think that could be easily
gleaned from the atom names, but be aware that in SHELX (or indeed a CIF)
the atom labels need
not reflect the atom types. G%##  is a perfect legal atom name in SHELX, but
not a helpful one.

So my comments on the example CIF you gave are
(1) get syntax right, the atom coordinate block is illegal because there
are 6 data items per line but only 5 descriptors
(2) bond length and angle information is unnecessary as it is derivative
information (though it 
causes no harm)

Regards Louis
=====================================================================
From:
Dr. Louis J. Farrugia
Department of Chemistry
University of Glasgow,
GLASGOW G12 8QQ
Scotland, UK.

Phone:  +44 (0)141 330 5137
FAX:    +44 (0)141 330 4888
email:  louis@chem.gla.ac.uk
Web  :  http://www.chem.gla.ac.uk/~louis/
=====================================================================

Reply to: [list | sender only]

• Prev by Date: RE: Getting a structure drawing program to create a "legal" CIF?
• Next by Date: Re: CIF: Getting a structure drawing program to create a "legal"
• Prev by thread: CIF: Gretep for Windows with CIF export
• Next by thread: RE: Getting a structure drawing program to create a "legal" CIF?
• Index(es):
  • Date
  • Thread