[phenixbb] Split Occupancy of a ligand and water

Brandon Goblirsch gobli033 at umn.edu
Mon Mar 28 12:40:08 PDT 2011


Currently I am have a structure which has a ligand bound at less than
full occupancy.  The ligand in this cause is covalently linked to a
CYS residue in the enzyme active site.  When the ligand is not
present, there are two well conserved waters in the active site in its
place.  Overall, I have a same space, split occupancy issue.  The
problem I am having now in phenix 1.7.460 is that I want to refine
(simultaneously) these water positions superimposed on the bound
ligand position (as both have less than 100% occupancy).  However,
upon refinement, the waters are always "kicked out" of position and
are not allowed to overlay with atoms within the bound ligand.  Does
anyone know how to get phenix.refine to accept the water and ligands
occupying the same coordinate space.  Obviously setting the ligand and
water positions to sub 100% occupancy does not do the trick.

Thanks for any help!!

Brandon Goblirsch
Research Assistant-Wilmot Lab
Biochemistry, Molecular Biology and Biophysics
5-230 Nils Hasselmo Hall
Minneapolis, MN 55455

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