hari jayaram wrote:

On Wed, Mar 3, 2010 at 7:13 PM, Nathaniel Echols mailto:[email protected]> wrote:

On Mar 3, 2010, at 2:36 PM, hari jayaram wrote: > Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . > I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2. > > I know the ccp4 coot does not come with python scripting support ..

That's understandable to some extent - ccp4 developers aren't pushing interactions with Coot like the PHENIX developers are. PE.

Hari is trying to break free of the codependency relationship. I'm not sure why ccp4 didn't build it with python support, but I think there is a misconception that it is an either/or proposition, which it isn't. I think all that needs to be done is to configure with " --with-guile --with-python=/prefix --with-pygtk=/prefix " Then in the coot shell script wrapper, I have export COOT_REFMAC_LIB_DIR=/prefix/coot/lib export COOT_PYTHON_DIR=/prefix/coot/python export PYTHONPATH=/prefix/lib/python2.6/site-packages:/prefix/lib/python2.6/site-packages/gtk-2.0:/prefix/coot/python:$PYTHONPATH to make it play nicely with phenix and refmac ( /prefix of course needs to be replaced with something real). Anyone is free to make use of, and improve, this: http://sage.ucsc.edu/fink_intel_10.6_only/dists/unstable/main/finkinfo/sci/c... I hope that might be of some use. Bill On Mar 3, 2010, at 4:13 PM, Nathaniel Echols wrote:

On Mar 3, 2010, at 2:36 PM, hari jayaram wrote:

...

Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2.

I know the ccp4 coot does not come with python scripting support ...the pymol integration seems fine , but coot just sits there with an empty window after a phenix.validate run.

Sorry, without Python embedded there's nothing you can do. Don't bother with the Coot packages distributed by CCP4 - use the binaries on Bill Scott's web page, or install it with Fink. I think the GUI used to display a warning if the Coot build was incomplete, but I never got this to work properly. Unfortunately several other people have run into this same problem, so I'll see if I can restore the Python check.

-Nat

-------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

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