Re: [ccp4bb]: planarity restraint in refmac5

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Huiying Li wrote:
> 
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> 
> On Fri, 13 Jul 2001, Bernhard Rupp wrote:
> 
> > My experience in agreement with Garib's advice is that the
> > X-ray weights are probably set high in default. I occasionally
> > run a regularization and refine few cycles with x-ray weights
> > low (Garib suggested 0.1, or lower at low res ( < 3.0)).
> >
> 
> Thank you for pointing this out. I re-run the same REFMAC5 refinement with
> a weight at 0.1, the distortion in geometry is negligible. The default
> of X-ray weight in CCP4i (0.5) is apparently way too high for the data
> resolution (2.1 A) I have.
> 
> Huiying Li


 I think that users should always look at their rms bond deviations
after the initial cycle. The required weight should more or less keep
this ~ 0.02; the expected standard deviation. The weight you need to set
to achieve this will vary with resolution, space group, and data
quality, and at least so far REFMAC5 makes no attempt to estimate a
better weight after a set of cycles; that is up to the user.

 Eleanor


> --------------------------------------------------
> Huiying Li, Ph. D
> Department of Molecular Biology and Biochemistry
> University of California at Irvine
> Irvine, CA 92697, USA
> Tel: 949-824-4322(or -1797);  Fax: 949-824-3280
> email: hli@bragg.bio.uci.edu
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