[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
values.
This topic is in the phenix.refine documentation:
http://phenix-online.org/documentation/refinement.htm#anch20
Please let me know if you have any further questions.
Pavel.
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
>
More information about the phenixbb
mailing list