[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
SO4
or
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".
Pavel
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