[phenixbb] Optimization of the mask parameters in PHENIX

Nathaniel Echols nechols at lbl.gov
Sun Apr 11 17:02:59 PDT 2010

On Sun, Apr 11, 2010 at 4:20 PM, Pascal Egea <pascal at msg.ucsf.edu> wrote:

> I am using the latest Phenix version (356) with the GUI and I would like to
> see the effect of optimization of the mask parameters.
> How can I do this with the GUI in the latest version ( I am also using the
> secondary structure restraints)
> in the manual I can see the command line
> phenix.refine model.pdb data.mtz optimize_mask=true however I don't see
> such option in the GUI (I can't see it  listed  in the whole list of
> commands)

I may have picked a poor caption for it.  It is labeled "Refine mask
parameters" and it will be in the "Miscellaneous settings" dialog, but you
need to set the user level to "advanced" to see it.  Opening
Settings->Search parameters and searching for "optimize" also brings it up.
 It is already on by default; apparently there is a slower protocol
"optimize_mask_thorough" which is still False, but Pavel will have to
explain what this means.

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