<div dir="ltr"><div>Hello to all our PDB experts,<br><br></div>If you didn&#39;t get this email from GitHub, could you take a look at<br>this bug report which has a nice clear reproducible test case?<br><a href="https://github.com/biopython/biopython/issues/441">https://github.com/biopython/biopython/issues/441</a><br><br>Thanks,<br><div><br>Peter<br><br><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Alexey Strokach</b> <span dir="ltr">&lt;<a href="mailto:notifications@github.com">notifications@github.com</a>&gt;</span><br>Date: Wed, Dec 10, 2014 at 7:57 PM<br>Subject: [biopython] PDBParser fails with error &quot;AttributeError: &#39;NoneType&#39; object has no attribute &#39;get_fullname&#39;&quot; (#441)<br>To: biopython/biopython &lt;<a href="mailto:biopython@noreply.github.com">biopython@noreply.github.com</a>&gt;<br><br><br><p>When I try to use PDBParesr to read the pdb for 3nh3 I get an error:</p>

<pre><code>AttributeError: &#39;NoneType&#39; object has no attribute &#39;get_fullname&#39;&quot;.
</code></pre>

<p>To reproduce the error:<br>
1) download &quot;3NH3.pdb&quot; from <a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=3NH3" target="_blank">http://www.rcsb.org/pdb/explore/explore.do?structureId=3NH3</a><br>
2) run the following code</p>

<pre><code>from Bio.PDB import PDBParser
parser = PDBParser()
structure = parser.get_structure(&#39;3nh3&#39;, open(&#39;3NH3.pdb&#39;, &#39;r&#39;))
</code></pre>

<p>Here is the full traceback:<br>
    Traceback (most recent call last):</p>

<pre><code>  File &quot;&lt;ipython-input-64-c2358d7c6b4e&gt;&quot;, line 1, in &lt;module&gt;
    structure = parser.get_structure(&#39;3nh3&#39;, open(&#39;3NH3.pdb&#39;, &#39;r&#39;))

  File &quot;/home/xx/anaconda/lib/python2.7/site-packages/Bio/PDB/PDBParser.py&quot;, line 86, in get_structure
    self._parse(handle.readlines())

  File &quot;/home/xx/anaconda/lib/python2.7/site-packages/Bio/PDB/PDBParser.py&quot;, line 109, in _parse
    self.trailer = self._parse_coordinates(coords_trailer)

  File &quot;/home/xx/anaconda/lib/python2.7/site-packages/Bio/PDB/PDBParser.py&quot;, line 225, in _parse_coordinates
    fullname, serial_number, element)

  File &quot;/home/xx/anaconda/lib/python2.7/site-packages/Bio/PDB/StructureBuilder.py&quot;, line 187, in init_atom
    duplicate_fullname=duplicate_atom.get_fullname()

  File &quot;/home/xx/anaconda/lib/python2.7/site-packages/Bio/PDB/Entity.py&quot;, line 210, in __getattr__
    return getattr(self.selected_child, method)

AttributeError: &#39;NoneType&#39; object has no attribute &#39;get_fullname&#39;
</code></pre>

<p style="font-size:small;color:rgb(102,102,102)">—<br>Reply to this email directly or <a href="https://github.com/biopython/biopython/issues/441" target="_blank">view it on GitHub</a>.<img alt="" src="https://github.com/notifications/beacon/AAD51-bg7rD8nko-Am2b97VmypGxOhsBks5nWJ05gaJpZM4DG0md.gif" height="1" width="1"></p>
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