You can also do group occupancy refinement: refine one occupancy for the whole ligand - in this case you don't need to put an ad hoc value. The current limitation (bug) is that the starting occupancy values in the input PDB file for that ligand must be all 1.0.

Pavel.


On 11/4/2008 11:26 AM, chern wrote:
How can I give occupancy 0.5 to my ligands and avoid occupancy refinement? Because the refinement gave me some atoms with occupancy 0.0 and adjacent atoms with occupancy 1.0 in the same ligand.
----- Original Message -----
From: Pavel Afonine
To: Ralf W. Grosse-Kunstleve ; PHENIX user mailing list
Sent: Tuesday, November 04, 2008 12:15 PM
Subject: Re: [phenixbb] refine occupancies for MET/MSE double conformations

Ralf,

it's not that uncommon. See for example:
http://www.rcsb.org/pdb/files/1ejg.pdb

Also, you may want to couple partially occupied residue's side chain with partially occupied water.

Pavel.


On 11/4/2008 9:36 AM, Ralf W. Grosse-Kunstleve wrote: 
Hi Tassos,

  
However, I want to refine my MET residues in double conformations, one
as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy
to start with.
    

In addition to what Pavel wrote: I just tried out the AMET BMSE mix
without giving any manual atom selections, and it works fine for me.
(P.S.: I'm thrilled to see this use of the
multiple-conformers-with-mixed-residue-names feature,
since it was a lot of work.)

Ralf
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