[phenixbb] selection usage

Pavel Afonine PAfonine at lbl.gov
Thu Sep 4 22:55:38 PDT 2008

Hi Mark,

sorry for delay with the reply - I'm out of office now and get to the Internet occasionally.

You need to do group occupancy refinement where one occupancy factor is refined for one selected group of atoms. All you need to do is to specify the selection of the group of atoms:

phenix.refine model.pdb data.mtz occupancies.group="chain X and resseq 1-5"

In this case phenix.refine will do all it normally does for occupancy refinement (do constrained refinement of occupancies for atoms in alternative conformations plus occupancies of atoms that are not equal to 1), plus it will refine one occupancy for atoms from 1 to 5 in chain X. This occupancy will be constrained between 0 and 1.

There is a problem here that I have to fix... If next time you run the refinement, the atoms that were previously refined with grouped occupancy option will be automatically picked up for individual occupancy refinement (because the default behavior that I described above).


----- Original Message -----
From: Mark Collins <mcollins at convex.hhmi.columbia.edu>
Date: Thursday, September 4, 2008 7:20 am
Subject: [phenixbb] selection usage
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> Hi All,
> The current phenix 1.3 release automatically selects alternate 
> conformations when refine  *occupancy is selected.
> How do I select a loop region (in low density) to refine the loop 
> occupancy without messing up the auto selection?
> Thanks in advance,  Mark 
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> phenixbb at phenix-online.org
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