[phenixbb] Refining an ion on a special position

Shane Caldwell shane.caldwell17 at gmail.com
Fri Jan 11 10:11:44 PST 2019

Hi phenixbb,

I've got a question related to refinement of an ion on a special position.
I have a structure with an atom placed squarely on the C2 axis. I've been
able to get a mostly-reasonable model by dropping in the ion at 0.5
occupancy and turning off repulsion for the ion in question, as Pavel
describes here
It almost completely works.

The thing I find now is that during refinement there can still be some
random drift of the atom away from the symmetry axis, splitting from its
symmetry ghost, while I know that it should stay perfectly coincident. My
resolution is 3.1 and there's no indication of a multiple conformation, so
a split isn't justified. The most parsimonious model should place the ion
exactly on the C2.

Is there any way to enforce that either 1. x, y = 0.0 in refinement, or 2.
the ion is constrained to the xyz of the symmetric version of itself. Both
should get to the same place, with the metal precisely on the axis, and
precisely over top of it's symmetric counterpart.


Shane Caldwell
Senior Fellow, Institute for Protein Design
University of Washington
Seattle, WA
scald at uw.edu
shane.caldwell17 at gmail.com
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