[phenixbb] getting phenix and coot to talk on OSX

Pavel Afonine pafonine at lbl.gov
Wed Jul 27 10:39:50 PDT 2011

> Aside from the problem that the program is looking for the geometry 
> libraries in one place and they are located in another place (that is 
> a CCP4 issue), I could not get Phenix (1.7.1-743) to communicate with 
> Coot.  I supplied the path to coot (/Applications/coot.app) and Phenix 
> started coot, but could not load the refinement information.  I tested 
> this during a refinement run on a 10.5.x machine, and from the 
> "Results" pane for a finished job under 10.6.8.  In the latter case, 
> pressing "Open in Coot" does fire up the program, but the molecule and 
> maps are not loaded.  On the other hand, choosing "Open in PyMOL" does 
> indeed display the molecule and maps.

You just described the problem that we had at two recent workshops: even 
though Coot was installed in /Applications/coot.app, PHENIX could not 
use it. Even providing the whole path to Coot in PHENIX GUI preferences 
did not help.


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