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 <novakw@wabash.edu> wrote:

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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