[BioPython] Extracting residue list from PDB

[Gad Abraham]

Hi,

I'm trying to extract a FASTA-like list of residues from a PDB file. It
doesn't seem to work correctly for some (e.g. 1n62, which comes out as
10 chains while it only has 6, and chain lengths are wrong too).

I'm using the following script based on the Structural Biopython FAQ:

#!/usr/bin/python

from Bio.PDB import *
import sys

parser = PDBParser()
structure = parser.get_structure(sys.argv[1], sys.argv[1])

ppb = PPBuilder()
for pp in ppb.build_peptides(structure):
   print len(pp),pp.get_sequence().tostring()
   print 


Any tips would be appreciated.

Thanks,
Gad
-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
gabraham at cs.rmit.edu.au
http://yallara.cs.rmit.edu.au/~gabraham
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++