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 <glasfeld@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

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org