[phenixbb] Split Occupancy of a ligand and water

Pavel Afonine pafonine at lbl.gov
Mon Mar 28 14:47:07 PDT 2011

  Hi Brandon,

you can do it - see two previous replies. If you still have any 
questions or problems then you can send me a PDB file, explain what and 
how you want to refine (point out relevant atoms, and how their 
occupancies are expected to be coupled), and then I will send you back a 
working example.


On 3/28/11 12:40 PM, Brandon Goblirsch 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

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