Hi Pascal,

just a remark: the next available nightly build will do optimization of mask parameters (r_solvent and r_shrink) by default. By "next" I mean whatever version appears after April 10.

Typically, optimization of mask parameters can make a visible difference for low resolution structures, lower than 3A. Sometimes it can be ~0.5A but I've seen cases with 2-3 % improvement.

Pavel.

On 4/11/10 4:20 PM, Pascal Egea wrote:

Dear All,

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)

Thanks in advance

--
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
314 Biomedical Sciences Research Building
office (310)-983-3515
lab (310)-983-3516
email pegea@mednet.ucla.edu
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