[Biopython-dev] [Bug 2910] New: Parsing some pdb files results in shorter peptide sequences than expected
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Wed Sep 9 15:18:01 UTC 2009
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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