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Re: Secondary Structure data from PDB file: msg#00018

java.bio.general

Subject: Re: Secondary Structure data from PDB file

Hi Andrew,

> Do I observe correctly that org.biojava.bio.structure.io.PDBFileParser
> does not currently handle secondary structure annotation (e.g. HELIX,
> SHEET, or TURN records),

The parser is fine, but this has been a missing feature so far.
To add support for this I just committed a patch to the biojava CVS.
The parser now
(optionally) can attach the secondary structure assignment that has
been provided by the author
of the PDB file to an amino acid.

See also
http://biojava.org/wiki/BioJava:CookBook:PDB:read

Andreas

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Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
+44 (0) 1223 49 6891



The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
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