[phenixbb] editing geometry restraints for C-beta deviation

Nathaniel Echols nechols at lbl.gov
Fri Aug 17 09:41:53 PDT 2012

On Fri, Aug 17, 2012 at 8:35 AM, Jeff Headd <jjheadd at lbl.gov> wrote:
> 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.

Technically, it will be restrained by a combination of the bond angle
and chirality restraints.  While it is in fact possible to adjust the
weights on these for specific atom selections, I don't recommend it,
for the same reason Jeff gives.

> 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.

Another suggestion from Markus Rudolph (whose message to the list was
bounced by the server):

"is there a slight chance you have an alternate conformation of, say,
20% for this Thr? I have had this happen to me before and after
inclusion of alternate conformations (based on density, of course),
the Cbeta deviation went away."

which is a very good idea, and quite common at high resolution (but
very easy to miss).


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