[phenixbb] Fixing a ligand by a symmetry axis

Simon Kolstoe s.kolstoe at ucl.ac.uk
Thu Nov 4 04:43:42 PDT 2010

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?



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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