[phenixbb] editing geometry restraints for C-beta deviation

Walter Novak novakw at wabash.edu
Fri Aug 17 09:57:30 PDT 2012


Thanks to all who replied! I refrained from going into many of the  
details in my initial post, and I am very thankful for al the  

This residue is in an interesting location as it contacts a mutation,  
so perhaps we can expect some deviation. I am fairly sure Markus is on  
the right track (thanks for forwarding this!). I have been  
experimenting with an alternate conformer (there is some positive  
difference density, but it isn't as clear cut as many of the other  
cases). When I do add an alt conf, the C-beta of the offender drops  
from a (horrific) 0.339 A to 0.259 A, which is just outside the  
allowed 0.25 A. I am much more comfortable with the latter, especially  
given the consensus reached by Ed, Jeff and Nat.

Thanks again to all.


On Aug 17, 2012, at 12:41 PM, Nathaniel Echols wrote:

> 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).
> -Nat
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Walter R.P. Novak
Byron K. Trippet 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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