[phenixbb] Fixing a ligand by a symmetry axis

Pavel Afonine pafonine at lbl.gov
Thu Nov 4 08:14:51 PDT 2010

  Hi Simon,

> I tried setting the occupancy to 0.5 however it still moved the atoms 
> out of position.

hm... then I don't know. If you send me the data and model and parameter 
file (if any used) then I will have a look and may be talk to collegues 
about this.

> 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?

Technically, there are many ways to force the molecule to stay where you 
want. But normally it shouldn't move in the first place, so it is good 
to find why it is moving out of place, and if we fail to find this out 
then we can force it.


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