[phenixbb] ncs restraints
Ralf W. Grosse-Kunstleve
rwgk at yahoo.com
Tue Dec 7 21:25:16 PST 2010
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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