[phenixbb] editing geometry restraints for C-beta deviation

Jeff Headd jjheadd at lbl.gov
Fri Aug 17 08:35:53 PDT 2012

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.


On Fri, Aug 17, 2012 at 11:07 AM, Walter R.P. Novak <novakw at 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
> ______________________________**_________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online.org/mailman/listinfo/phenixbb>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120817/186e88bd/attachment.htm>

More information about the phenixbb mailing list