[phenixbb] Modifications for Ca-binding site

Keller, Jacob kellerj at janelia.hhmi.org
Mon Dec 28 18:44:13 PST 2015

I am getting a lot of problems with my calcium binding sites--there is clear density for the calciums and the protein side chains, but Phenix keeps sucking the side chains out of their density towards the calciums and also the calciums show some positive difference density, perhaps due to too-high b-factors (or potentially partial occupancy by Na?). I think what might work best is to turn off the Ca-O bond length restraints somehow, but don't see where/how to do that. I tried releasing them from geometrical restraints, but that made things worse, since things went haywire in the sidechains themselves.

Is it possible to make Phenix ignore the Ca-O bond distance restraints?


Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kellerj at janelia.hhmi.org

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