[phenixbb] Fixing coordinates in phenix.refine_gui

Nathaniel Echols NEchols at lbl.gov
Tue Jun 2 10:00:15 PDT 2009

On Jun 2, 2009, at 9:48 AM, Pavel Afonine wrote:
> 1) start phenix.refine GUI;
> 2) load in your model and data;
> 3) Under "Refinement settings" click (once or twice, figure out) on  
> "Individual sites". This will pop up the selection window  
> "Selections for individual site refinement". Type in atom selections  
> for atoms that you want to refine (or that you don't want to refine  
> with leading "not").

The easier way to edit the selection: Settings menu -> Atom selections  
-> Coordinate refinement (the first selection is for the "individual  
sites" strategy, although this isn't very clearly labeled right now).

One other clarification: "None" is the default for many of these  
selections, but that usually means that phenix.refine will pick the  
selection automatically.  I believe that for the individual sites  
strategy, "None" is equivalent to "all".  (Use "not all" to select  
zero atoms.)

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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