[phenixbb] Occupancy refinement

Nathaniel Echols nechols at lbl.gov
Thu May 31 14:41:25 PDT 2012

On Thu, May 31, 2012 at 11:55 AM, Jerome Nwachukwu <JNwachuk at scripps.edu> wrote:
> I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this?

You have to set the altloc identifier for the two conformations - it's
the column next to the residue ID, i.e.:

ATOM   5085  N  AALA   270      19.772  -6.267  40.250  0.75  5.17
ATOM   5090  N  BALA   270      19.733  -6.282  40.242  0.25  5.04


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