[phenixbb] exploring the conformational space of sidechains
pafonine at lbl.gov
Thu Oct 27 00:19:58 PDT 2011
if you are still interested, tomorrow I can write a 10-line Python
script that will do what you want.
I will probably need to know what you mean by "different but also
reasonable sidechains conformations" (just to eliminate guesses)?
For each residue I can generate an ensemble of plausible rotamers (based
on Molrpobity library). Obviously, some of them will be clashing with
the neighbor atoms, which I can resolve by 1) simply not adding such
rotamers, or 2) doing some geometry regularization to ease the clashes.
Any of two are trivially done. Then I simply write a new PDB file with
such side chain ensembles.
So, please give me more information about how you want to have it done,
and confirm that you still want it, and I will do it tomorrow (this is
somewhat inline with what I am doing right now anyway).
On 10/26/11 6:06 PM, Francois Berenger wrote:
> Is there a way to do this with Phenix?
> I.e., from a given model, obtain models with
> different but also reasonable sidechains conformations.
> N.b.: I don't have X-ray data so I am looking
> for a geometric thing, and I'm OK
> if the model's backbone undergoes some small
> movement because of the sidechains having moved.
> Thanks a lot,
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