[phenixbb] How to fix c-beta deviation?

Robert Immormino immormino at gmail.com
Wed Apr 6 07:20:24 PDT 2011


While phenix.refine is an incredible powerful tool for structure
refinement, as Nat said earlier some re-building may be required.
Without re-building addition of ramachandran restraints may only mask
problems rather than fix them.  Fortunately, Cbeta deviations are
quite sensitive and as far as I know are truly independent structure
validation measures see:


quoting from the abstract:
Cbeta deviation is sensitive to incompatibilities between sidechain
and backbone caused by misfit conformations or inappropriate
refinement restraints.

Good Luck,

On Wed, Apr 6, 2011 at 9:50 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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