[phenixbb] side-chain on special position.

Pavel Afonine pafonine at lbl.gov
Thu Feb 1 17:31:01 PST 2018


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:* 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,
>
> Aaron
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20180201/1001c427/attachment.htm>


More information about the phenixbb mailing list