[phenixbb] Phenix and COOT Together on a Mac (and Probe too?)

Nathaniel Echols nechols at lbl.gov
Tue Aug 31 13:09:50 PDT 2010

On Tue, Aug 31, 2010 at 12:54 PM, Joseph Noel <noel at salk.edu> wrote:
> One thing that seemed to solve all the problems at once was to completely
> remove any reference to the COOT path in the Phenix preferences! Is that
> weird? When I removed it completely only leaving the path to PYMOL then COOT
> is working just fine in conjunction with Phenix and even the Probe issues
> have disappeared. Prior to this, I was tried two different paths to COOT.
> 1. /sw64/bin/coot

This in theory should work, but there is at least one way for it to
break (involving a mixup between 32-bit and 64-bit Python modules and
Fink vs. system Python).  I suspect that is what is breaking on your

> 2. /Applications/coot.app/Contents/MacOS/coot

If you got the app bundle from the CCP4 homepage this will definitely
not work, unfortunately - command-line arguments don't get passed to
Coot itself.

> Neither behaved but if I don't specify anything it works.

Type "phenix.find_coot_command" to see exactly what it's using - on my
system, this is /usr/local/bin/coot.


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