[phenixbb] Phenix version 1.7-650 and Pymol

Nathaniel Echols nechols at lbl.gov
Wed Feb 2 12:56:34 PST 2011

On Wed, Feb 2, 2011 at 12:42 PM, Ben Eisenbraun
<bene at hkl.hms.harvard.edu> wrote:
> Nat is talking about a different PyMOL.  The binary at
> /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe generated the error, but
> you're showing the info for one installed from YUM.

Oops, I totally missed the different paths.  That's definitely the problem.

> In any case, the problem is that the PyMOL shipped _with_ PHENIX is a
> 32-bit binary, even in the 64-bit download.

Perhaps it would save everyone trouble if we stopped distributing
PyMOL with Phenix?  Version 0.99 is so obsolete anyway that I'd really
prefer that everyone obtain the latest version separately.

> I got a window on my OS X machine the other day telling me that PHENIX
> would prefer to use a newer MacPyMOL if it could find one in /Applications.
> Can I configure this to find the newer MacPyMOL in a different path?  How
> about on linux?  That might be another possible solution to Leonid's
> problem.

Yes: Preferences->Graphics->Full path to PyMOL.  On Mac, this could
either be the native .app bundle, or a Unix-style executable installed
from the open-source distribution.  However, 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.


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