On Wed, May 7, 2014 at 2:05 PM, Marcelo Carlos Sousa <Marcelo.Sousa@colorado.edu> wrote:

It turned out that if you point phenix (in preferences) to the wrapper script inside the coot application package:
/Applications/ccp4-6.4.0/coot.app/Contents/coot/bin/coot
and start the application by clicking on the Phenix icon and then opening refinement results in coot, then the coot dictionaries do not load and there is a problem

However, if you start phenix form the terminal then everything is fine.
Finally, if you point phenix to a different file in the coot application package:
/Applications/ccp4-6.4.0/coot.app/Contents/MacOS/coot

This is already handled automatically - I didn't think anyone would dig into the .app bundle for the specific command. If you simply specify /Applications/ccp4-6.4.0/coot.app (or any other .app), Phenix will look for Contents/MacOS/coot inside.

-Nat