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. Cheers, Paul 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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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 To: [email protected] 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.