[Biojava-l] Different chain lengths using struc.getChainByPDB and iterating over a structure and it's chain

[Andreas Prlic]

Hi Rafael,


>
> suppose the following PDB file:
>     ...

>
> 1) If I use
>
> //struc being the parsed pdb file
> returnChain = struc.getChainByPDB("A", 1);
>
> I get chain A EXCEPT everything after the TER (ZN and ADE is excluded
> in this example).

This seems wrong. You should get the full chain here. TERs are getting  
ignored. Let me check what might cause this. You are on the latest  
version from svn?

> 2) If I iterate over the complete file using something like
>
> //struc being the parsed pdb file
> int nrModels = struc.nrModels();
>
> for (int modelNr = 0; modelNr < nrModels; modelNr++) {
> List<Chain> chains = struc.getModel(modelNr);
> int nrChains = chains.size();
> for (int chainNr = 0; chainNr < nrChains; chainNr++) {
>
> //this chain contains also the ZN and the ADE

That's what I would expect...

Andreas






>
>
>
>
> So maybe I am getting something wrong here. Is this effect wanted by
> the PDB parser?
>
>
> Thanks!
>
>
> Raphael
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