[Biojava-l] Newbie struggling with secondary structure

[Andreas Prlic]

Hi Tjaart,

The PDB parser currently does not parse all of the header - the HELIX 
and SHEET lines containing the author's secondary
structure assignments are are currently ignored.

> An alternative is simply to write a class which reads all the lines 
> starting with HELIX or SHEET

for the moment this might be a solution

> and somehow parse them into meaningful results.

what is meaningful? :-) - in case you want to add the data  to the 
AminoAcid objects,
you might want to have a look at the PDB file parser and write a patch 
that reads the lines and stores the
data in the amino acids. let me know if you need help.

Cheers,
Andreas

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