[phenixbb] ncs restraints

Paul Adams pdadams at lbl.gov
Tue Dec 7 19:43:27 PST 2010

Hi Tim,

  increasing the coordinate_sigma to 0.5 will make the restraint considerably looser. However, at 3.0A resolution I'd want to be convinced that this change made things better by looking at the R-free (i.e. I'd expect that tighter restraints were more appropriate at this resolution). If there are areas where there are detectable differences between the NCS copies you might want to exclude them from the restraint selection and keep the rest tight.


On Dec 7, 2010, at 7:31 PM, Timothy Springer wrote:

> 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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Paul Adams
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Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
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