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