[phenixbb] Limit Ramachandran restrain to certain region

Nathaniel Echols nechols at lbl.gov
Tue Apr 3 13:47:36 PDT 2012

On Tue, Apr 3, 2012 at 1:38 PM, Nian Huang <huangnian at gmail.com> wrote:
> Is it possible to limit Ramachandran restrain to specified residues in
> phenix.refine? I have a couple of loops with very poor density. The
> refinement process always made some residues fall out of ramachandran
> plot no matter how I tightened the weight and adjusted the residues
> back. Because the diffraction is about 2.3 A, I don't want the
> ramachandran restrain to impact the rest of structure. Thanks.

Which version of Phenix are you using?  If it's 1.7.1 or earlier, you
need to update to the latest version ASAP, because this will probably
fix the problem.

If you're already using the latest version, the parameter
rama_selection will do what you want.  But you really shouldn't need
Ramachandran restraints at 2.3A resolution - and I'd advise against
using them entirely, at any resolution.  They're just too dangerous
and lead to unnatural structures.  You also probably don't want to be
running real-space refinement for this structure.  However, when
you're rebuilding, using Coot's Ramachandran restraints together with
its local real-space refinement should be sufficient to give you a
good starting model, which Phenix will hopefully not screw up.


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