[phenixbb] Split Occupancy of a ligand and water

Katherine Sippel katherine.sippel at gmail.com
Mon Mar 28 13:45:17 PDT 2011

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,


On Mon, Mar 28, 2011 at 2:40 PM, Brandon Goblirsch <gobli033 at 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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