Occupancy Refinement

Yoram Puius puius at aecom.yu.edu
Sun Jun 14 14:30:32 EST 1998

Merilyn Blair-Johnson wrote:

> Hi all,
>  Can someone tell me how to refine the occupancy of ligands soaked into
> a crystal structure using x-plor?
>  I have just been using an occupancy of 1 but am not sure if the sites
> are fully occupied.

The code will look something like

    xrefin                      {*occupancy refinement*}
     optimize group
      q=( segid "ALT1" and resname CPD ) {* Ligand A *}
      q=( segid "ALT2" and resname CPD ) {* Ligand B *}

 or, if your ligand is residue 1001,

  q=(resid 1001)

As I'm sure you know, B-factors and occupancies are highly correlated.
Frequently, you can't tell the difference between a disordered molecule
full occupancy and a well-ordered molecule with partial occupancy.

Unless you have a real biochemical reason to believe that your molecule is

partially occupied (e.g. alternate conformations interfering with your
concentrations of ligand less than 10x the binding constant, etc.) I would

leave the occupancy at 1.0.

Just my 20 millidollars,

Yoram A. Puius                Albert Einstein College of Medicine
6th year M.D.-Ph.D.           Department of Biochemistry
mailto:puius at aecom.yu.edu     1300 Morris Park Avenue, Bronx, NY  10461
"My enlightenment is proceeding wonderfully." - Donald Barthelme

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