<div dir="ltr">Hi Guoying,<div><br></div><div>Can you share the code and the exact FileParsingParameters that you are using to parse your file? </div><div><br></div><div>2JA5 does not have coordinates for chain N. The following code still can parse out a structure object. BioJava complains, but with a different error message than you reported. The error message that I get seems like over-reporting from BioJava and it probably should be a warning, rather than an error. </div><div><br></div><div>Having said that, your exception is a NullpointerException and at least with the code below I don't get that...</div><div><br></div><div><pre style="color:rgb(0,0,0);font-family:Menlo;font-size:12pt">FileParsingParameters params = <span style="color:rgb(0,0,128);font-weight:bold">new </span>FileParsingParameters();<br>params.setStoreEmptySeqRes(<span style="color:rgb(0,0,128);font-weight:bold">true</span>);<br><br>AtomCache cache = <span style="color:rgb(0,0,128);font-weight:bold">new </span>AtomCache();<br>cache.setUseMmCif(<span style="color:rgb(0,0,128);font-weight:bold">false</span>);<br>cache.setFileParsingParams(params);<br><br>StructureIO.<span style="font-style:italic">setAtomCache</span>(cache);<br><br>Structure bioAssembly = StructureIO.<span style="font-style:italic">getBiologicalAssembly</span>(<span style="color:rgb(0,128,0);font-weight:bold">"2ja5"</span>,<span style="color:rgb(0,0,255)">1</span>);</pre></div><div><br></div><div>Andreas</div><div><br></div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 15, 2015 at 3:21 AM, Guoying Qi <span dir="ltr"><<a href="mailto:gqi@ebi.ac.uk" target="_blank">gqi@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><p style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small">Hi there,</p><div>I am using BioJava 4.1.0 and got the following error message for PDB 2ja5 when no ATOM for chain N, P and T when <span style="font-family:Monaco;font-size:11px">StoreEmptySeqRes is on.</span></div><div><span style="font-family:Monaco;font-size:11px"><br></span></div><div>I am sure the parser should cope with this kind of issues.</div><div><br></div><div>Could somebody have a look?</div><div><br></div><div>Thanks.</div><div><br></div><div>Guoying</div><p style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small"><span><br></span></p><p style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small"><span>Exception in thread "main" </span><span>java.lang.NullPointerException</span></p><p style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small"><span></span>at org.biojava.nbio.structure.io.PDBFileParser.storeUnAlignedSeqRes(<span>PDBFileParser.java:3026</span>)</p><p style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small"><span></span>at org.biojava.nbio.structure.io.PDBFileParser.triggerEndFileChecks(<span>PDBFileParser.java:2973</span>)</p><p style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small"><span></span>at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(<span>PDBFileParser.java:2769</span>)</p></div></blockquote></div><br><br clear="all"><div><br></div>
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