[phenixbb] getting phenix and coot to talk on OSX

Nathaniel Echols nechols at lbl.gov
Wed Jul 27 11:12:23 PDT 2011

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

> 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

(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


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