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 [email protected]
On Sun, Apr 11, 2010 at 4:20 PM, Pascal Egea
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. -Nat
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 [email protected] mailto:[email protected]
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participants (3)
-
Nathaniel Echols -
Pascal Egea -
Pavel Afonine