[phenixbb] Occupancy Refinement of substrate and product occupying the same coordinates.

Pavel Afonine PAfonine at lbl.gov
Mon Jul 12 21:29:05 PDT 2010

Hi Joe,

> I have a crystal structure which I believe involves the substrate and 
> product of the enzymatic reaction occupying the same space within the 
> active site. Ideally, I would like to refine their occupancies to sum 
> to a value less than or equal to 1, 

you can do it in phenix.refine. If you assign one molecule an altLoc A 
and the other one altLoc B, and have them under the same residue name 
and chain id, their occupancies will be refined and the sum of them will 
be constrained to exactly 1. This is  explained in phenix.refine manual:


If you still having trouble with this, then you can just send me your 
PDB file or its fraction containing the ligands in question, and I will 
help you from there.


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