[phenixbb] real-space refinement

Wed Nov 6 09:15:42 PST 2013

Well, I am dealing with a case (2.0 A data) in which overall refinement goes well (R/Rfree about 0.20/0.23), but the fit of side chains to electron density appears to be a little bit worse than it could be (many instances of atoms which appear a bit off the density centroid, easily corrected by RSR in Coot, for instance). Moreover, I found that the current phenix version gives me an Rfree about 1.5 % higher than an older version (dev-1343) did, with exactly the same input, and I suspect the reason may be the missing RSR component.

Regards,
Oliver

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  PD Dr. Oliver H. Weiergräber
  Institute of Complex Systems
  ICS-6: Structural Biochemistry
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
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________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine [pafonine at lbl.gov]
Sent: Wednesday, November 06, 2013 5:28 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] real-space refinement

Hi Oliver,

> beginning with phenix 1.8.3, the individual_sites_real_space option will not run globally if, e.g., R < 0.25.
> Is there a way to force the original behaviour?

no. What's the reason to do this?

Pavel
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