[phenixbb] getting phenix and coot to talk on OSX

Nathaniel Echols nechols at lbl.gov
Wed Jul 27 11:18:07 PDT 2011

Sorry for the multiple emails, but I just remembered that the
procedure below is more trouble than necessary - if you launched
Phenix from the icon, you can still get to the console by running
Apple's Console.app, which is in /Applications/Utilities, or this

open -a Console

This should have all of the Coot output.


On Wed, Jul 27, 2011 at 11:12 AM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Tue, Jul 26, 2011 at 11:42 PM, Harry Greenblatt
> <Harry.Greenblatt at weizmann.ac.il> wrote:
>>     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

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