[BioPython] PDBParser, chain iterator problem. Terminating just after TER record

[Lee, Byung-chul]

Hi biopython users,

During paring the pdb files, I met a ridiculous parsing result.

I coded my program like below:

from Bio.PDB import *
p = PDBParser()
s= p.get_structure('test','pdb1j1t.ent')
m0 = s[0]
for r in m0['A']:
print r

then the result was obtained like :
...
<Residue GLU het= resseq=231 icode= >
<Residue THR het= resseq=232 icode= >
<Residue ASN het= resseq=233 icode= >
<Residue CA het=H_ CA resseq=301 icode= >

But in the pdb file, the TER record was written before Residue CA like
below:
...
ATOM 1763 OD1 ASN A 233 -3.371 16.572 33.547 1.00 51.28 O
ATOM 1764 ND2 ASN A 233 -3.068 17.873 31.741 1.00 49.95 N
ATOM 1765 OXT ASN A 233 -6.247 19.343 31.607 1.00 51.21 O
TER 1766 ASN A 233
HETATM 1767 CA CA A 301 31.453 10.121 13.116 1.00 15.05 CA
HETATM 1768 S SO4 302 21.891 21.921 14.715 1.00 50.50 S

Thus I think BioPython's model iterator must stop before <Residue CA
het=H_ CA resseq=301 icode= >, and I want to know why this happens and
how I can solve this.

Regards,

Byung-chul Lee

-- 
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The important thing is not to stop questioning.
                               : Albert Einstein

Byung chul Lee 
                at Detp. BioSystems KAIST, Korea
                                  Ph.D candidate
                                  82-42-869-4357
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