[phenixbb] Sulfate ion on 2-fold axis

Pavel Afonine pafonine at lbl.gov
Sat Apr 30 22:50:18 PDT 2011


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.


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 <moloch525 at gmail.com>
>     *To:* phenixbb at phenix-online.org
>     *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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