[phenixbb] occupancy refinement question

Pavel Afonine PAfonine at lbl.gov
Mon Aug 27 14:21:18 PDT 2007

Hi John,

here is the complete refinement example emulating exactly what you are 
trying to do:


Just look at the files and run "run" file to see the result. It takes 
less than 20 secs to run on my computer. All it does, it refines one 
occupancy for alternative conformation A and one occupancy per 
alternative conformation B. Note the selections I used to specify the 

Please let me know if you have any questions.

John Bruning wrote:
> Hi,
> I have a ligand with dual conformations.  I want to do group occupancy
> refinement on the conformers (each conformer is one group).  I keep
> having trouble.  The ligand is one chain named chain E and conformer 1
> has residue name ADRG and conformer 2 has residue name BDRG.  This is
> what I suppose my .def file should have in it:
> occupancies {
>       individual = None
>       group = "chain E and resname ADRG"
>       group = "chain E and resname BDRG"
>       one_occupancy_group_per_residue = True
>     }
> When I run this it tells me I have an ambiguous selection.
> Any ideas why this isn't working and how I can change my .def file to
> make it work?
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