[phenixbb] exploring the conformational space of sidechains

Pavel Afonine pafonine at lbl.gov
Thu Oct 27 00:19:58 PDT 2011

Hi Francois,

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:
> Hello,
> 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,
> F.

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