[phenixbb] Fixing a ligand by a symmetry axis

Pavel Afonine pafonine at lbl.gov
Wed Nov 3 10:04:26 PDT 2010

  Hi Simon,

you may find this helpful:



On 11/3/10 9:41 AM, Simon Kolstoe wrote:
> Dear Phenix bb,
> I have a palindromic ligand bound to my protein that crosses a 
> symmetry axis. Although the head-group that is in close contact with 
> the protein refines beautifully (in phenix..refine version 1.6.4 run 
> from the command line on a mac), the atom closest to the symmetry axis 
> get knocked away from the equivalent atom that it binds to on the 
> other side of the symmetry axis. Is there any way of stopping 
> phenix.refine from refining the atoms closest to the symmetry axis, or 
> should I just manually position the wayward atom in the appropriate 
> orientation prior to my structure deposition?
> Thanks,
> Simon

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