[Biojava-l] PDBFileParser and identifying atoms in ligands

Andy Thomas-Cramer thomascramera at dnastar.com
Thu May 6 16:50:15 UTC 2010

>From a PDB file, I can identify which atoms are in ligands, and which
are in residues in the chain. The chain atoms end with the TER record.


>From the BioJava API, I can distinguish as well -- if it's an amino
sequence and the automatic alignment between SEQRES and ATOM sequences
is successful. 


Is there a way through the API to identify atoms in ligands, when the
chain is not an amino sequence or alignment fails? It looks like the TER
record is ignored by PDBFileParser.


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