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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 />
  </fieldset>


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