[phenixbb] Question about structure quality

Edward A. Berry BerryE at upstate.edu
Tue Apr 5 14:11:10 PDT 2011

After fixing the Ramachandran with restraints, I would recommend refining
several cycles without restraints before depositing to see how many
outliers stay in the allowed region.  The ramachandran is often used
as a measure of model quality, and you might just fool the end user
into using your structure instead of a better model which
has slightly worse ramachandran but much better than yours would be
without restraints.


Pavel Afonine wrote:
> 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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