[phenixbb] occupancy

Pavel Afonine PAfonine at lbl.gov
Sun Aug 23 19:11:41 PDT 2009

Hi Maia,

occupancies of atoms in alternative conformations are refined in 
phenix.refine by default. If your PDB file contains properly defined 
(with altLoc identifiers) atoms in alternative conformations, then their 
occupancies are the subject of constrained occupancy refinement, where 
occ(A)+occ(B)=1 and occupancies of all atoms belonging to an occupancy 
group are equal. For this scenario you don't need to do anything apart 
from having correctly formatted PDB file with alternative conformations 
defined in it.

You can also ask phenix.refine to refine occupancies of selected atoms 
"completely freely" - without any constraints or restraints. Limits on 
occupancy values will not be imposed during minimization, but somewhere 
in refinement macro-cycle to ensure that the refined occupancies are 
withing [occ_min, occ_max], where occ_min and occ_max are user-defined 

This topic is in the phenix.refine documentation:

Please let me know if you have any further questions.


On 8/22/09 2:03 PM, Maia Cherney wrote:
> Hi Pavel,
> is it possible to refine individual occupancies of atoms in alternative 
> conformations?
> Maia

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