[BioPython] BioPDB problem

[Thomas Hamelryck]

On Friday 18 June 2004 12:01, Hua Wong wrote:
> I have a PDB file that count 3145 atoms [1...3145], and using BioPDB I try
> to get all the coordinate.

One possibility might be that the PDB file contains disordered atoms. They 
will be packed in one DisorderedAtom object, which in term holds the Atom 
objects.

The method residue.get_unpacked_list() returns all the individual atoms, and
'unpacks' disordered atoms. 

So if this is indeed the case, do the following:
Replace this line:

for atom in residue.get_iterator():

by:

for atom in residue.get_unpacked_list():

There might be other reasons, ie. a buggy PDB file. 
Try running the parser in 'strict' mode:

parser=PDBParser(PERMISSIVE=0)

This will throw an exception if the PDB file is buggy.

Hope this helps,

-Thomas

-- 
Thomas Hamelryck
Bioinformatics center
University of Copenhagen      
Universitetsparken 15 Bygning 10                 
2100 København Ø, Denmark
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http://www.binf.ku.dk/users/thamelry/