[BioRuby] bio.pdb doubt

K. Shameer shameer at ncbs.res.in
Thu Feb 21 12:31:45 UTC 2008

Hi Alex,

Thanks for the  detailed explanation.

> 1. How do you know what the solvent is? In 99% cases it's HOH but not
> always. Sometimes you have all sorts of other weird molecules floating
> around. If you siphon off all HOH molecules into a separate 'solvent'
> data structure you'll loose information for some structures.

This true. I agree with you. But it will be great if we could have a way
to handle solvent as a separate data structure rather than part of the
chain. This will be again useful for people who wanted to add water /
remove water as a requirement for some analysis (for example Molecular

> 2. The HETATM/ATOM distinction is tricky as well. Some HETATM records
> (including the solvent in some PDB files) are given distinct chain ids
> and in some cases do represent linear chain like molecules. Bound DNA
> for instance: ATOM? HETATM? Chain? Not a chain? There is no consistent
> representation of these things in (legacy) PDB files so any choice you
> make will be a compromise.

I agree with you in the case of NA and in the data inconsistency issues
with PDB files. But in case of  protein complexes HETATM tags are  very
helpful. For example I used to extract ligands(small molecules) from set
of related PDB (ligand + receptor complex) files to use as a library of
substrates for docking studies. I dont know how easily I can code this
with BioRuby/Bio.PDB.  I haven't tried this with bioruby. But I will try
it out very soon.

> That said, if you want to have a poke through the PDB parser and make
> some changes then be my guest. It's been a while since I did any PDB
> stuff (and god-willing it will be a while until I do some more!) so
> it's an area that could probably do with a fresh pair of eyes.

That will be interesting, provided if you could offer some offline
help/directions to start with. Infact I am specifically interested in
something that has not taken up by any of the Bio-toolkit libraries :).
Can we (Alex, Jan, all other bioruby pros and Shameer) work on to develop
a module that integrated both Bio.Pdb and Bio-Graphics module to generate
modular topology diagrams ? Please let me know your comments, we can
discuss and work on this :) !!!


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