[phenixbb] occupancy refinement

Pavel Afonine pafonine at lbl.gov
Mon Aug 12 13:31:56 PDT 2013

Hi Georg,

> However I want to do this  in the future giving a occ.params file or 
> with the gui.
> a) In gui  under refinement settings --> mody selection for 
> -->ocupancies--> individual selection I put SO4
> I get an error saying AtomSelectionError

Did you just put
resname SO4
You should use "resname SO4" (quotes are optional).

> b) adding an occ.params file to the input files
>     occupancies {
>       individual = resname SO4
> ...
his looks just fine and should work. Did you undo your attempt to 
specify selections using "a)" ?

What happens if you run it in the command line:

phenix.refine model.pdb data.mtz occ.params


> leads to phenix error
> RuntimeError: atom selection syntax error at word "so4". Atom 
> selection string leading to error: SO4

I can reproduce this error only if I use "SO4" instead of correct 
"resname SO4".


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