On Tue, Jul 26, 2011 at 11:42 PM, Harry Greenblatt
The version of coot that is available from CCP4 is 0.6.2 (3562). This was shown on the CCP4 download page for Mac OSX, as one of the additional things you might want. The advantage of this precompiled binary is that is claims to be compatible back to 10.4.x.
That's what I'm using - I can't rule out that something has changed since 1.7.1, however. The only change I'm aware of offhand is that it should now find /Applications/coot.app automatically (although given how unreliable that distribution has been, I'm not sure it's a good idea).
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.
Okay, the way to test this is a little bit convoluted if you used the graphical installer - try this from the command line: source /Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix_env.sh phenix (if you're using tcsh, just remove ".sh" from the end of the source script) Then re-open your refinement results, click "Open in Coot", and send me the console output. On my computer it ends with this: Running python script /Users/nat/phenix/src/phenix/wxGUI2/Coot.py Could not import coot_python module! PHENIX GUI extensions will be disabled. Loading PHENIX Coot extensions... xml-rpc server running on port 40092 -Nat