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

Nathaniel Echols nechols at lbl.gov
Mon Aug 30 16:45:04 PDT 2010

On Mon, Aug 30, 2010 at 4:14 PM, Joseph Noel <noel at salk.edu> wrote:
> I am having trouble getting COOT to link up with Phenix. I know that Bill
> Scott's fink version of COOT breaks the link but I have also tried the stand
> alone latest version for Mac OSX without success.

Which stand-alone version?  Did you try this one already?


I am using this (also on Snow Leopard) and it has been working great;
the only thing I can think to suggest is to make sure that you've set
the Coot path to /usr/local/bin/coot in the PHENIX preferences.  (This
is probably what it will use automatically anyway, but if you have set
another path by mistake, or you have multiple Coot installations, it
might use the wrong one.)  For what it's worth, I've also had good
luck with the Fink installation, aside from unrelated flakiness in
Fink.  On the other hand, I don't do very much model-building.

There is one other very remote possibility, which is that you have
conflicting Python modules installed.  What is the output when you run
this command?

coot --script $PHENIX/phenix/wxGUI2/Coot.py

Usually there is an obvious error message towards the end of the
console output.  (Actually, if you're starting the GUI from the
command line, you may already be getting the same output when you
launch Coot.)  It might be worth trying this both with /sw64/bin/coot
and /usr/local/bin/coot, in case one is more informative.

> I can also run probe independently in COOT using the script suggestion for
> the .coot file from the MOLPROBITY web site. However, after several checks
> of bad contacts the system freezes at the level of XQuartz and I have to
> kill X-Windows to start over. I don't know if this is in someway linked to
> the problem getting COOT and Phenix to talk to one and other but I thought I
> would throw it out there.

I don't know if this is related, but it sounds like a completely
different problem than what we usually encounter - I haven't noticed
anything similar.  Which version of XQuartz are you using, and what
kind of graphics card?


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