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Issue #2910 has been updated by Lenna Peterson.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15369?detail_id=1674">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Resolved</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Migrated to github:</p>
<p><a class="external" href="https://github.com/biopython/biopython/issues/992">https://github.com/biopython/biopython/issues/992</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2910#change-15369">Bug #2910: Bio.PDB build_peptides sometimes gives shorter peptide sequences than expected</a></h1>
<ul><li>Author: Christian Schaefer</li>
<li>Status: Resolved</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: 1.49</li>
<li>URL: </li></ul>
<p>Parsing the one-letter sequence for a specific chain out of a given pdb file often seems to result in shorter sequences than expected.</p>
<p>The following code demonstrates this behavior for structure 1a2d chain A. Aminoacid #118 VAL after the HETATOM (<a class="issue tracker-1 status-5 priority-7 priority-highest closed" title="Installation problem (Closed)" href="https://redmine.open-bio.org/issues/117">#117</a>) block is missing in the result.</p>
<p>------------------CODE----------------<br />from Bio.PDB.PDBParser import PDBParser<br />from Bio.PDB.Polypeptide import *</p>
<p>parser = PDBParser()<br />ppb = PPBuilder()<br />structure = parser.get_structure('tmp', '1a2d.pdb')<br />polypeptides = ppb.build_peptides(structure<sup><a href="#fn0">0</a></sup>['A'])<br />sequence = str(polypeptides<sup><a href="#fn0">0</a></sup>.get_sequence())</p>
<p>print sequence<br />------------------CODE----------------</p>
<p>Another example is structure 13gs chain C and D. Both sequences are ECG, the code above however returns only CG.<br />So this behavior seems to be indepedent from a present HETATOM block.<br />This bug is also present in version 1.51.</p>
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