Based on information at
I've come in late on this discussion.
0. There are CIF checkers available for free on http://www.iucr.org. If a file doesn't obey these it isn't a CIF. No arguments
A. I think that Jmol should be very strict on CIF syntax. In which case the file should start with data_foo where foo is a unique ID within the file
B. mmCIF is a *superset* of basic CIF syntax and vocabulary. mmCIFs must be syntactically valid
C. CIF has the concept of dictionary definition language. DDL1 (for small molecules) is simpler than DDL2 for macromolecules.
D. there is a cascading set of dictionaries. These dictionaries have items some of whose semantics Jmol will require, others (like telephone of author) it probably doesn't. Jmol can choose which it wishes to honour. They should be interpreted consistently with the spec.
Best
P.
http://ndbserver.rutgers.edu/NDB/mmcif/index.html
and
http://ndbserver.rutgers.edu/mmcif/examples/index.html
I'd say mmCIF is a subset of CIF and has to still follow the same basic rules. All the descriptions at
http://ndbserver.rutgers.edu/mmcif/dictionaries/html/cif_mm.dic/Groups/index.html
involve "data items" -- that is, categories within "data_" so "data_" still has to be the first non-comment item in the file.
I think this file, even if mmCIF, is invalid.
Bob Hanson
Miguel wrote:
Tamas wrote:
Miguel,
CIF and mmCIF are too different formats. mmCIF is for macromolecular CIF, the extension of the original CIF format to proteins etc. Cf.: http://www.ccp4.ac.uk/dist/html/mmcifformat.html
Tamas, I am not familiar with the details ... I thought that mmCIF was basically an extension to CIF that defined additional attributes and tags to support the needs of (and correct some of the problems with) PDB files. Given the iucr's stance on .CIF files, and their involvement in mmCIF, I would be quite surprised if they relaxed their position on grammar compliance with mmCIF. ... perhaps others can assist in clarifying this ...
As an interim measure ... put the line data_ At the top of your file and Jmol will recognize it as a .cif file and will *hopefully* read it in.
Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] -----
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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