Hi Aaron, exclude that side chain from non-bonded repulsion with the symmetry mate by using custom_nonbonded_symmetry_exclusions="chain A and resseq 123 and sidechain" If using CL simply add the above parameter (after editing the selection appropriately). If using GUI, find this parameter in "All parameters" and type in atom selection. Let me know if you have any questions or problems doing this! Also, could you please send me the PDB file off-list (or just a part of it containing that residue)? I'd like to automate this in phenix.refine so that in future the program takes care of this automatically. Thanks, Pavel On 2/1/18 14:00, Keller, Jacob wrote:
Model two conformations?
JPK
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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:* [email protected] [mailto:[email protected]] *On Behalf Of *Aaron Oakley *Sent:* Thursday, February 1, 2018 4:37 AM *To:* [email protected] *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,
Aaron