[phenixbb] ncs restraints

Timothy Springer springer at idi.harvard.edu
Wed Dec 8 05:23:21 PST 2010

Thanks, I believe this is an important tip.

On Dec 8, 2010, at 12:25 AM, Ralf W. Grosse-Kunstleve wrote:

> 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.
> Ralf
> 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?
> Thanks,
> Timothy A. Springer, Ph.D.                                    
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