[Biopython-dev] [Biopython (old issues only) - Bug #2910] (Resolved) Bio.PDB build_peptides sometimes gives shorter peptide sequences than expected

[redmine at redmine.open-bio.org]

Issue #2910 has been updated by Lenna Peterson.

Description updated
Status changed from New to Resolved
% Done changed from 0 to 100

Migrated to github:

https://github.com/biopython/biopython/issues/992

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Bug #2910: Bio.PDB build_peptides sometimes gives shorter peptide sequences than expected
https://redmine.open-bio.org/issues/2910#change-15369

* Author: Christian Schaefer
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.49
* URL: 
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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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