[phenixbb] coot integration require coot with python?

William G. Scott wgscott at chemistry.ucsc.edu
Wed Mar 3 17:02:21 PST 2010

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:


I hope that might be of some use.


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
> NEchols at lbl.gov
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