Thanks for the help. I tried setting the occupancy to 0.5 however it still moved the atoms out of position. Is there a way I can prevent phenix.refine from moving any of the ligand atoms in the last round of refinement, or alternatively add a restraint that will apply across the symmetry axis? Thanks, Simon On 3 Nov 2010, at 17:04, Pavel Afonine wrote:

Hi Simon,

you may find this helpful:

http://www.phenix-online.org/pipermail/phenixbb/2009-December/003070.html

Pavel.

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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is the NCS turned off?