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

+++++++++++++++++++++++++++++++++++++++++++++++++

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

+++++++++++++++++++++++++++++++++++++++++++++++++

The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future.

*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

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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

+++++++++++++++++++++++++++++++++++++++++++++++++

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

+++++++++++++++++++++++++++++++++++++++++++++++++

The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future.

*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