[phenixbb] Question about structure quality

Nathaniel Echols nechols at lbl.gov
Tue Apr 5 14:05:01 PDT 2011

On Tue, Apr 5, 2011 at 1:57 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> - Often using Ramachandran restraints fixes the problem right away, so I
> would probably do it first, and then walk through the list of outliers that
> you had before refinement run with Ramachandran restraints, and see *how*
> these outliers were fixed. Nat's suggestion should work too but might
> require more up-front work.

It will "fix" the problem only to the extent that the Ramachandran
statistics/plot look better - this does not automatically mean that
the structure is more accurate.  When you are refining against one of
the primary validation criteria, more up-front work is essential.
(The restraints will also not automatically fix every problem, so if
you blindly turn them on without any rebuilding, the result will
likely be worse than if you correct as many residues as possible


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