[BioPython] Sequence Numbering in PDB-Files

[kaoskrew.de]

Hi Everyone!

I'm pretty new in terms of biopython, so it might be, that I just didn't
get into the right parts of the manual yet.

So first I'd like to refer to this email from the archive:
http://portal.open-bio.org/pipermail/biopython/2004-November/002452.html
I have the same problem. Because I need a list of all positions in a 
pdb-structure
including the position and the icode, I'd need to find out the start- 
and end-
position.

Additionally I didn't found out yet how it's possible for me to iterate 
over all
positions or how I even could get all of the positions. Yet the way I 
chose
looks like that:

from Bio.PDB.PDBParser import PDBParser
p = PDBParser(PERMISSIVE=1)
structure_id="1nrn"
filename="PDBs/1nrn.pdb"
s=p.get_structure(structure_id,filename)
print s
model=s[0]
chain_L=model["L"]
res=chain_L[10]
test=res.get_id()
print test[1]

That would lead to an output of just the position. But it's not really 
working
out yet. I had to submit the chain, which should be found automatically,
iterating over the positions stopped somewhere in between the sequence
without concrete reason and the icode was totally ignored.

So, if anyone has worked with this problem already, help would be 
greatly
appreciated! If I just didn't find the right page in the manual, please 
give me
a hint.

Thanks,
Tobias Zimmer
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