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

Pavel Afonine pafonine at lbl.gov
Thu Jan 29 09:56:39 PST 2009

Hi Stephen,

there is a file "/phenix/phenix/refinement/__init__.params" that defines 
all default parameters for phenix.refine. I don't like the idea of 
changing it, but this is the place where if you change something then 
this will be global.


PS. Why you need to turn the occupancies refinement off by default? If 
you have alternative conformations or some atoms with partial 
occupancies, then I don't see any argument against of refinement their 
occupancies all the time you run refinement.

On 1/29/2009 9:26 AM, Stephen Graham wrote:
> Hi all,
> 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.
> Cheers,
> Stephen
> 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...

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