[Biojava-l] PDB parsing: Calculate absolute atom numbers of a chain.

Andreas Prlic andreas.prlic at gmail.com
Wed Mar 4 15:38:26 UTC 2009


Hi Umanga,

You will need to use the getPDBCode() method to obtain the PDB residue
number as well as the chain ID to select the residue in Jmol.

Andreas




2009/3/4 Ashika Umanga Umagiliya <aumanga at biggjapan.com>:
> Greetings all,
>
> From a database; I retrieve PDB-id ,chainID and epitope positions.These
> epitope positions are calculated relative to its Chain.
> I want to select these epitope positions (residues) in JMol.But in jmol the
> select query support only absolute residues numbers.
>
> Ex:
> CHAIN L : residues 10,12,13,15 (relative to chain L)
> But in PDB file (in JMOL) the values are 210,212,213,215 - this are what I
> want to calculate?
>
> Anyway to calculate this?
>
> Thanks in advance,
> Umanga
>
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