[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?
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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