Hi,

occupancy refinement in phenix.refine does not use information about special positions. So if it sees an atom (or groups of atoms) having partial occupancy it will refine them to be any number between 0 and 1. This is in my to-do list to fix one day.

Currently, you need to turn off the occupancy refinement for these atoms manually using "occupancies.remove_selection".

However, if the input occupancy is set to 1 then internally phenix.refine will do the right thing with respect to special position (it will apply the multiplicity factor), and it will not refine it. The downside of doing it this way is that this is not what PDB expects.

Pavel.


On 4/30/11 10:07 PM, Ralf W. Grosse-Kunstleve wrote:
This should work as you expect in more recent phenix versions. My recommendation is to install 1.7.1 and then try again. -- phenix versions can co-exist. Just make sure you source the phenix_env of the version you want to use.
Ralf

From: J. Fleming <[email protected]>
To: [email protected]
Sent: Saturday, April 30, 2011 9:13 PM
Subject: Re: [phenixbb] Sulfate ion on 2-fold axis

Hi all,

  I have a sulfate ion sitting on a 2-fold axis of symmetry.  If I set all the atom occupancies to 0.5 and refine using phenix.refine (Phenix v. 1.5-2) the occupancies are changed to 0.00 for the sulfur, 1.00 for three of the oxygen's, and 0.72 for the fourth oxygen.  Can anyone explain this?

Thanks in advance,
Jon