[phenixbb] side-chain on special position.

Keller, Jacob kellerj at janelia.hhmi.org
Thu Feb 1 14:00:55 PST 2018

Model two conformations?


Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004

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From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Aaron Oakley
Sent: Thursday, February 1, 2018 4:37 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] side-chain on special position.

Hello fellow  Phenix-ers,

I have a structure I am trying to finish in Phenix.refine

The is one problem: a glutamate residue sitting on a crystallography 2-fold axis
with partial occupancy (picture attached). This residue and its symmetry mate appear to take turns sitting
at this position: filling the density leads to severe collision with its symmetry mate.
Building the side-chain with occupancy 0.5 doesn’t seem to help, as the residue is pushed
out of density during refinement.

Any work-arounds?

Thanks all,


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