[phenixbb] group on special position

Dr. Karine Röwer karine.roewer at gmail.com
Wed Aug 12 22:37:31 PDT 2020

Hi Arthur,
from the way I used to work in small molecule crystallography, I'd set the
occupancy of the atoms on the symmetry axis to 0.33, and keep only one of
the other three O atoms with an occupancy of 1. I'd expect phenix to
generate the other two O atoms via symmetry operators, and applied to the
atoms on the symmetry axis, you should get a total occupancy of 1. Does
that help?

On Thu, Aug 13, 2020 at 2:56 AM Arthur Glasfeld <glasfeld at reed.edu> wrote:

> I’ve run into a situation where I think I have a phosphate sitting on a
> 3-fold axis, where the P to O1 bond lies on the axis and the atoms O2, O3
> and O4 are in symmetry-related positions. The data go to 1.6 Å, so it looks
> pretty convincing.  I’m refining this in Phenix and have tried some tricks
> with occupancy - fixing the atoms at 0.33, but I get a lot of positive
> density in the Fo-Fc map and large B-factors.  I’ve looked around but am
> not finding ideas on how to model this correctly in my structure file - the
> references I find are for monoatomic ions.  Any advice would be welcome.
> Thanks,
> Arthur
> *****************
> Arthur Glasfeld
> Reed College
> Portland, OR 97202
> Office: (503)517-7679
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