[phenixbb] Question about structure quality
Pavel Afonine
pafonine at lbl.gov
Tue Apr 5 13:57:12 PDT 2011
Hi Jason,
> The Ramachandran statistics are poor; I've seen worse published, but
> it would be wise to fix these. I'm assuming you don't have a
> high-resolution structure that you can use as a reference model - this
> is usually the best option. Otherwise, adding Ramachandran restraints
> will probably help a lot, but you should first fix all outliers
> manually in Coot (also applying real-space refinement with Coot's
> Ramachandran restraints turned on), as the default potential is very
> tight and can pull residues the wrong way if they're starting from a
> very bad position.
- 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.
- Run refinement with weights optimization (optimize_wxc=true);
- Use NCS if available;
- Secondary structure restraints should definitely help, but:
-- you need to have secondary structure well defined in your input
model if you want phenix.refine to pick it up automatically (and
correctly), or alternatively
-- define it manually in a parameter file and supply to phenix.refine.
Pavel.
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