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

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