[phenixbb] coot links on Mac

Nathaniel Echols nechols at lbl.gov
Thu Jul 29 13:50:33 PDT 2010

On Thu, Jul 29, 2010 at 1:26 PM, Joseph Noel <noel at salk.edu> wrote:

> I noticed that coot behaves unusually on the MacOS version of phenix. It
> will open when you hit the button in the GUI but it will not open any of the
> files you specify. Just the main coot window which you then have to load
> everything as you would normally if running coot stand alone.

This usually means that the Python embedded in Coot isn't linked correctly
(on Linux, it usually means Python wasn't even included).  One way to tell
is to look on the toolbar in Coot - if it doesn't have a button that says
"Connected to PHENIX" (or something like that), my extension module failed.
  Which version are you using?  I believe the most recent binary on Bill
Scott's page may have this problem, but I'll double-check.  I use Fink (
http://www.finkproject.org/) to install and update Coot, and this has always
worked quite well as long as Fink doesn't crash on me.

Also, I noticed that when you run coot from the gui link on MacOS that after
> manipulating the structure for rebuilding, etc it will freeze requiring a
> force quit of x-windows to recover. However, if I open coot directly from my
> xterm on MacOS it works fine and no freezes.  Just a note. Love the program!

This I haven't heard before.  We have to tamper with the environment
variables to get Coot to launch from inside Phenix, at least on Linux, and
this may have side effects.  Where does the console output from Coot end?

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