[phenixbb] How to fix c-beta deviation?

Jeff Headd jjheadd at lbl.gov
Wed Apr 6 07:50:26 PDT 2011

Hi Jason,

C-beta deviations are often coupled with rotamer outliers, or even an
incorrect rotamer. One technique that Paul Emsley showed me for
correcting C-beta deviations in Coot is to mutate the offending
residue to ALA, then regularize and real-space refine the region
(including 2-3 residues on either side). This will hopefully allow for
the mainchain to find a more suitable position, without a misplaced
sidechain trapping it in a false minima. After that, you can mutate
the residue back to what it should be, and look for the best rotamer
given the density and the new mainchain orientation.


On Wed, Apr 6, 2011 at 6:50 AM, Jason <phenix.upitt at gmail.com> wrote:
> Hi,
> I have tried to regularize my protein structure in coot and use ramachandran
> restrain to improve statistics (and then release them). However, I can not
> make the c-beta deviation be zero. Is there some special way to improve
> c-beta deviation? Thanks.
> ======================
> Jason
> Structural Biology Department
> University of Pittsburgh
> ======================
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