Hi Maia, if you are using "ordered_solvent=true" then there is no guarantee that this specific water or its assigned occupancy will be preserved. Currently the only way to keep it is to refine your model until you are done, and only then add that water and do a quick refinement with "ordered_solvent=false". Water updating machinery is not smart about spacial positions. Pavel. On 4/5/11 8:26 PM, Ralf W. Grosse-Kunstleve wrote:
Hi Maia,
I changed the phenix.refine behavior back in Dec 2009. If you have any phenix version released in 2010 or 2011 (dev-268 or later), setting the occupancy to 0.50 should do what you expect.
Ralf
----- Original Message ----
From: Maia Cherney
To: Pavel Afonine ; PHENIX user mailing list Sent: Tue, April 5, 2011 8:03:44 PM Subject: Re: [phenixbb] occupancy on a special position Hi,
I have a water on a two fold axis, I gave it occupancy 0.50, but the program makes it 1.0. I know this was discussed before, but we have to abide by the PDB rules, that is to have this occupancy =0.5.
Could you please, fix this problem.
Maia