[phenixbb] fixing geometry for deposition

Raja Dey rdey at usc.edu
Wed Nov 18 08:54:29 PST 2009

I have 4 monomers(all same) and 2 dna molecules in the AU. Density for 1 dna having 2 alternate conformations is weak. The rest is fine. I have not included the dna in ncs parameter file. Also, some of the residues showing different side chain conformaions are excluded form ncs.  


----- Original Message -----
From: Pavel Afonine <PAfonine at lbl.gov>
Date: Tuesday, November 17, 2009 4:58 pm
Subject: Re: [phenixbb] fixing geometry for deposition
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> > You might also consider excluding the regions with poor geometry 
> from 
> > the NCS groups, to see if they are in fact different. You are 
> also 
> > forcing NCS regardless of the RMS distance. I would refine a few 
> > rounds without NCS and with the default refinement parameters, 
> and 
> > then then turn the NCS back on. Look in the .geo file for 
> excessive 
> > distances, and examine these regions in Coot using the NCS ghosts 
> and 
> > maps to decide if they should be excluded from the NCS groups.
> Thanks Kendall, it is very good point. We should probably do 
> something 
> like this to automatically adjust NCS restraints during refinement.
> Pavel.

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