I'm in dialog with RCSB on this and will get back to folks when I've
gotten more information.
Bob
Egon Willighagen wrote:
On Monday 17 April 2006 11:20, Jaime Prilusky wrote:
According to Eric Martz:
Several errors in PDB files were reported to RCSB recently. Often their
response is "it is fixed in the mmCIF". CIF is a burning issue for now
(for FirstGlance), but it is GREAT that Jmol will be able to read mmCIF
in future. Are you reporting the errors you found in mmCIF files to RCSB?
([EMAIL PROTECTED])
There's more than one way of writing a valid mmCIF file, and RCSB is
intermixing them. Probably the parsing problem you report is due to
alternative mmCIF 'flavors'.
What about parsing PDB's XML? These files (should) reflect all fixes and
improvements from mmCIF files in an easy to parse XML format. Structures
in PDBML format are available from RCSB PDB website or ftp, and from OCA's
mirrors http://bip.weizmann.ac.il/oca-bin/send-xml?1d66
I have looked at them earlier, and noted that while the syntax is 'easier'
(i.e. XML based), it is really the data structure that is the problem.
I have not checked the files from the URL you gave, but the XMLs from pdb.org
itself are really not easier to parse. As long as the informat is split up
over several data substructures, and one has to get those bits of information
together, it does not really matter wether it is PDB, mmCIF or XML syntax.
The XML Schema for Exchange Data dictionary is available from
http://pdbml.rcsb.org/schema/pdbx.xsd
Egon
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