[BioRuby] bio.pdb doubt

K. Shameer shameer at ncbs.res.in
Thu Feb 21 10:27:03 UTC 2008


> I shouldn't have posted code without testing first!


> The problem is that the PDB parser reads the solvent (water) molecules
> into a separate chain. So in this case we have the protein chain and
> the water 'chain'. My naive multichain? method then reports you have
> two chains.

Is this something unusual ? In a structural bioinformatics scenario
solvent/water belongs to the HETATM definition. I am not able understand
the logic behind the consideration of a ATOM records as well as HETATM
records as part of chain.

> A reasonable workaround is to check each chain to see if it actually
> contains any residues. We can test this my retrieving the residue
> array for each chain and checking if its size is greater than 0. So
> our multichain? method becomes a bit more complex:
> DISCLAIMER: You still might run into edge cases with things like bound
> ligands and so on. If these are small peptides they will be considered
> as separate chains even if you don't think they should be. One way
> round this would be to alter the residue size test in the code above
> to look for chains with more than x residues (where x could be 5,10,30
> or so) to filter out very small chains. You'll have to make that call
> according to your needs and particular research.

This alright with me. In case of small peptides, I need them to be
considered as separate chains only.

Thanks for the detailed explanation. I modified the script as you suggest.
W00t!!! My first bioruby script (that not mentioned in tutorial) is up and
running - Thank you Alex, Thanks Naohisa :) !!!!
K. Shameer
Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in

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