[phenixbb] exploring the conformational space of sidechains

Nathaniel Echols nechols at lbl.gov
Wed Oct 26 19:54:05 PDT 2011

On Wed, Oct 26, 2011 at 6:06 PM, Francois Berenger <berenger at riken.jp> 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.

There is a set of modules that is used for rotamer sampling, but it's
basically ignorant of proper packing - we rely on maps and real-space
refinement to make sure everything ends up in the right place, and the
minimizer will have trouble fixing severe overlaps.  You're probably
better off looking at a program designed for this, like SCWRL or
Rosetta.  However, if you want to try something really fast and messy,
this will do approximately what you want:

phenix.pdbtools model.pdb min_rotomer_distortion=True regularize_geometry=True

which will change all sidechains to a minimally different rotamer,
then minimize against geometry restraints.  There is also a
max_rotomer_distortion keyword.  We use these to test convergence of
various refinement methods, but the models they produce probably
aren't very realistic.  The code that does all of this could easily be
adapted to sample more comprehensively (look at
$PHENIX/cctbx_project/mmtbx/command_line/lockit.py for an example of
rotamer iteration), but it'll have the same limitations.


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