[phenixbb] occupancy on a special position

Pavel Afonine pafonine at lbl.gov
Tue Apr 5 21:25:00 PDT 2011

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.


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<chern at ualberta.ca>
>> To: Pavel Afonine<pafonine at lbl.gov>; PHENIX user mailing list
>> <phenixbb at phenix-online.org>
>> 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

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