[Biopython-dev] [Bug 2910] New: Parsing some pdb files results in shorter peptide sequences than expected

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2910

           Summary: Parsing some pdb files results in shorter peptide
                    sequences than expected
           Product: Biopython
           Version: 1.49
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: critical
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: schafer at rostlab.org


Parsing the one-letter sequence for a specific chain out of a given pdb file
often seems to result in shorter sequences than expected. 

The following code demonstrates this behavior for structure 1a2d chain A.
Aminoacid #118 VAL after the HETATOM (#117) block is missing in the result. 

------------------CODE----------------
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Polypeptide import *

parser = PDBParser()
ppb = PPBuilder()
structure = parser.get_structure('tmp', '1a2d.pdb')
polypeptides = ppb.build_peptides(structure[0]['A'])
sequence = str(polypeptides[0].get_sequence())

print sequence
------------------CODE----------------

Another example is structure 13gs chain C and D. Both sequences are ECG, the
code above however returns only CG.
So this behavior seems to be indepedent from a present HETATOM block.
This bug is also present in version 1.51.


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