Hi Wally,
We don't use an explicit C-beta positional restraint in Phenix, so there
isn't any parameter you could change that would change its treatment as an
outlier. Also, the C-beta deviation metric is done independent of geometry
restraints, and is a static evaluation function.
Much like rotamers, having an occasional outlier given very high resolution
data is not a problem, and you can just ignore it if you believe your data
supports the deviated chemistry. Validation metrics only reflect general
guidelines for what is acceptable, and often true outliers can be some of
the most interesting parts of a structure.
Jeff
On Fri, Aug 17, 2012 at 11:07 AM, Walter R.P. Novak
Hi,
I have a relatively high-resolution (1.1 A) structure and one threonine residue has a C-beta deviation outlier that I cannot prevent via any traditional means. I would like to try to restrain the C-beta deviation for this residue by scaling the geometry restraints for this residue, but I am not sure of how I should define the restraint for C-beta. Any suggestions are greatly appreciated.
Thanks, Wally
-- Walter R.P. Novak Assistant Professor of Chemistry Wabash College 301 W. Wabash Avenue Crawfordsville, IN 47933 Phone: 765-361-6407 Fax: 765-361-6149
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