[phenixbb] Optimization of the mask parameters in PHENIX

Pavel Afonine PAfonine at lbl.gov
Sun Apr 11 18:26:28 PDT 2010

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.


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 at mednet.ucla.edu <mailto:pegea at mednet.ucla.edu>
> ------------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100411/436bb963/attachment-0003.htm>

More information about the phenixbb mailing list