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Issue #3146 has been updated by Vincent Davis.
<ul>
<li><strong>File</strong> <a href="https://redmine.open-bio.org/attachments/download/1791/pdb2p0i.ent">pdb2p0i.ent</a> added</li>
</ul>
<p>I am getting very different results on current biopython.</p>
<p>from Bio.PDB import PDBParser<br />parser = PDBParser()<br />from Bio.PDB.DSSP import DSSP<br />structure=parser.get_structure("2p0i","pdb2p0i.ent")</p>
<p>/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 27135.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 27164.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 27180.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 27185.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain E is discontinu!
ous at line 27207.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 27234.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain G is discontinuous at line 27263.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 27293.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 27315.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PD!
BConstructionWarning: WARNING: Chain B is discontinuous at lin!
e 27461.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 27612.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 27738.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 27866.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 27987.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstruct!
ionWarning: WARNING: Chain G is discontinuous at line 28094.<br /> PDBConstructionWarning)<br />/Users/vincentdavis/anaconda/envs/py35/lib/python3.5/site-packages/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 28225.<br /> PDBConstructionWarning)</p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/3146#change-15336">Bug #3146: DSSP ungraceful failure</a></h1>
<ul><li>Author: Patrick empty</li>
<li>Status: New</li>
<li>Priority: Low</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: 1.53</li>
<li>URL: </li></ul>
<p>The DSSP annotator should probably fail gracefully when the PDBParser and DSSP disagree about the existence of a residue at a certain position. Here, DSSP reports values for residue 115 of chain A, while the PDBParser throws a key error.</p>
<p>from Bio.PDB import PDBParser<br />parser = PDBParser()<br />from Bio.PDB.DSSP import DSSP<br />structure=parser.get_structure("2p0i","pdb2p0i.ent")<br />model=structure<sup><a href="#fn0">0</a></sup><br />dssp=<abbr title="model, "pdb2p0i.ent"">DSSP</abbr><br />Traceback (most recent call last):<br /> File "<stdin>", line 1, in <module><br /> File "/usr/lib/pymodules/python2.6/Bio/PDB/DSSP.py", line 175, in <i>init</i><br /> res=chain[res_id]<br /> File "/usr/lib/pymodules/python2.6/Bio/PDB/Chain.py", line 71, in <i>getitem</i><br /> return Entity.__getitem__(self, id)<br /> File "/usr/lib/pymodules/python2.6/Bio/PDB/Entity.py", line 38, in <i>getitem</i><br /> return self.child_dict[id]<br />KeyError: (' ', 115, ' ')</p>
<blockquote><blockquote><blockquote>
<p>model['A'][114]</p>
</blockquote></blockquote></blockquote>
<p><Residue GLN het= resseq=114 icode= ></p>
<blockquote><blockquote><blockquote>
<p>model['A'][116]</p>
</blockquote></blockquote></blockquote>
<p><Residue TYR het= resseq=116 icode= ></p>
<blockquote><blockquote><blockquote>
<p>model['A'][115]</p>
</blockquote></blockquote></blockquote>
<p>Traceback (most recent call last):<br /> File "<stdin>", line 1, in <module><br /> File "/usr/lib/pymodules/python2.6/Bio/PDB/Chain.py", line 71, in <i>getitem</i><br /> return Entity.__getitem__(self, id)<br /> File "/usr/lib/pymodules/python2.6/Bio/PDB/Entity.py", line 38, in <i>getitem</i><br /> return self.child_dict[id]<br />KeyError: (' ', 115, ' ')</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1791/pdb2p0i.ent">pdb2p0i.ent</a>
(2.24 MB)<br />
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