[phenixbb] editing geometry restraints for C-beta deviation

Walter Novak novakw at wabash.edu
Fri Aug 17 10:10:43 PDT 2012

Thanks Nat, I will try this immediately.


On Aug 17, 2012, at 1:06 PM, Nathaniel Echols wrote:

> On Fri, Aug 17, 2012 at 9:57 AM, Walter Novak <novakw at wabash.edu>  
> wrote:
>> 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).
> A simple trick you could try is to reduce the occupancy of the Thr in
> the single-conformer model (somewhere in the 0.5-0.75 range is good)
> and re-calculate the maps.  Sometimes this makes the difference map
> clear enough to show where the second conformation goes, since it
> isn't quite as flattened out by presence of the (full-occupancy)
> primary conformation.
> -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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