[phenixbb] Site-wide defaults for phenix.refine parameters

Nathaniel Echols NEchols at lbl.gov
Thu Jan 29 09:45:00 PST 2009

On Jan 29, 2009, at 9:26 AM, Stephen Graham wrote:
> Apologies if I've missed this in the documentation, but is there any
> way to set 'site-wide' defaults for, say, phenix.refine?  That is, I'd
> like to modify the default parameters for phenix.refine so that
> occupancy refinement is turned off by default, the
> output.serial_format is different, geo files aren't created, always
> use F/SIGF not I/SIGI, etc.

This is possible to some extent with the phenix.refine GUI, although  
it's very much a work in progress.

> P.S.  I know I can change this by hand in my .def file and then
> propagate the .def file through subsequent rounds of refinement for a
> given project.  It would just be nice to have my default personal
> preference parameters set (~/.phenix?) so I don't need to change them
> each time I start a new project...

Right now the (new) GUI creates a directory ("phenix") in each project  
that contains various meta-information, and a sub-directory "defaults"  
which contains any files to be used automatically.  It will also read  
in a global defaults file if you specify one in the preferences.

For the command-line version, couldn't you just alias phenix.refine to  
"phenix.refine ~/.phenix/refine_defaults.def"?

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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