[phenixbb] ncs restraints

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Tue Dec 7 21:25:16 PST 2010

Hi Tim,

If you start from nearly identical copies (due to previous refinement), in the 
absence of a strong signal from the data, it is expected that the copies remain 
fairly similar even if you increase the sigma / lower the weight. We just added 
a new feature to phenix.refine that could be useful to introduce differences 
between the NCS copies, guided by the model density through a new real-space 
refinement protocol: strategy=individual_sites_real_space plus 
real_space_refinement.mode=lockit. At your resolution it is turned on by 
default. I.e. to try it out all you need to do is get dev-602 or higher and run 
phenix.refine again. Only trouble, those installers aren't generally visible 
since there were some minor problems, but watch out for a new one soon.


>From: Timothy Springer <springer at idi.harvard.edu>
>To: phenixbb at phenix-online.org
>Sent: Tue, December 7, 2010 7:31:44 PM
>Subject: [phenixbb] ncs restraints
>Hi, I am using NCS restraints for 4 copies of a molecule at 3.05 Å. We are using 
>the standard weights:
>      coordinate_sigma = 0.05
>      b_factor_weight = 10
>and the 4 molecules look identical. What are suggested values for looser 
>restraints?  One of my colleagues said that varying them did not make a 
>difference- ncs was still very strict. Is there a way to make them less strict?
>Timothy A. Springer, Ph.D.                                    
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