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?
Cheers,
Karine
On Thu, Aug 13, 2020 at 2:56 AM Arthur Glasfeld
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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