[phenixbb] editing geometry restraints for C-beta deviation

Nathaniel Echols nechols at lbl.gov
Fri Aug 17 10:06:55 PDT 2012

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.


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