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). Pavel. 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.