[phenixbb] group on special position

Arthur Glasfeld glasfeld at reed.edu
Wed Aug 12 17:53:51 PDT 2020

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.


Arthur Glasfeld
Reed College
Portland, OR 97202
Office: (503)517-7679

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