[Biojava-l] PDBFileParser Error for PDB files without ATOM part for some chains defined in the header

Guoying Qi gqi at ebi.ac.uk
Tue Sep 15 10:21:52 UTC 2015

Hi there,

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 StoreEmptySeqRes is on.

I am sure the parser should cope with this kind of issues.

Could somebody have a look?



Exception in thread "main" java.lang.NullPointerException

at org.biojava.nbio.structure.io.PDBFileParser.storeUnAlignedSeqRes(PDBFileParser.java:3026)

at org.biojava.nbio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2973)

at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2769)
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