[phenixbb] Refinement - addition/clarification

Pavel Afonine pafonine at lbl.gov
Tue Mar 31 11:15:43 PDT 2015


A small addition/clarification:


>> How do tell phenix.refine to not move my HEM ligand around?
>
> yes, you can exclude selected atoms from refinement of coordinates
>
> in Phenix refinement GUI:
>
>    Refinement settings -> Modify selection for: XYZ coordinates -> 
> Edit -> type atom selection in "Edit selected" field (under XYZ 
> refinement) like "chain A and resseq 1" or "chain A and resname ATP"

this will define what atoms to refine. In example above only coordinates 
of atoms belonging to "chain A and resseq 1" will be refined. You can 
negate it "not (chain A and resseq 1)" so that all but coordinates of 
atoms belonging to "chain A and resseq 1" will be refined.

Pavel



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