[phenixbb] Phenix version 1.7-650 and Pymol

Nathaniel Echols nechols at lbl.gov
Thu Feb 3 10:29:30 PST 2011

On Thu, Feb 3, 2011 at 9:24 AM, Ben Eisenbraun <bene at hkl.hms.harvard.edu> wrote:
>> Phenix really should look in more places before giving up and start
>> 'phenix.pymol'; I'll start by checking in /usr/bin, /usr/local/bin,
>> /sw/bin/, and /sw64/bin, but we can probably examine the shell
>> environment for aliases too - Ralf did something like this for Coot,
>> which has worked reasonably well for most situations.
> Finding it in the environment or via an environment variable would be my
> preferences, since I'd like to configure it in one place for all my users.

I definitely think we should be able to do this, but I forgot about
the method for setting Phenix preferences globally (for all users).
There are two environment variables, PHENIX_GUI_DEFAULT_PREFS, and
PHENIX_GUI_SITE_PREFS; the first is read in before an individual
user's preferences, the second is read in afterwards (so it will
override whatever the user has set).  So you could, for instance,
create a file named "phenix_prefs.linux-i386.eff", and put this in it:


and then:

setenv PHENIX_GUI_SITE_PREFS /some/path/phenix_prefs.linux-i386.eff

Or something like that.  I added this mechanism so industry users
could route bug reports to a local contact instead of bouncing off the
corporate firewall, but it's potentially useful for any other large
installation.  I'll put something in the documentation about this.


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