Use different altloc tags in the PDB (Column 18). For example:

HETATM 2142  O  AHOH  1009       1.332 -11.668  14.957  0.50  6.57           O  
HETATM 2143  O  BLIG  1010       7.403  -7.755  -0.773  1.00 29.28           O

Then it will know they don't occupy the same space at the same time. As a word of warning the occupancy refinement of two proximal atom that don't have the same residue number can sometimes add up to more than 1 so check to make sure the model makes physical sense.

Hope this helps,

Katherine

On Mon, Mar 28, 2011 at 2:40 PM, Brandon Goblirsch <gobli033@umn.edu> wrote:

Hello,

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
--
Brandon Goblirsch
Research Assistant-Wilmot Lab
Biochemistry, Molecular Biology and Biophysics
5-230 Nils Hasselmo Hall
Minneapolis, MN 55455
(612)624-0141
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