[phenixbb] coot links on Mac

William G. Scott wgscott at chemistry.ucsc.edu
Sun Aug 1 23:00:40 PDT 2010

On Jul 29, 2010, at 1:50 PM, Nathaniel Echols wrote:

> On Thu, Jul 29, 2010 at 1:26 PM, Joseph Noel <noel at salk.edu> wrote:
>> I noticed that coot behaves unusually on the MacOS version of phenix. It
>> will open when you hit the button in the GUI but it will not open any of the
>> files you specify. Just the main coot window which you then have to load
>> everything as you would normally if running coot stand alone.
> This usually means that the Python embedded in Coot isn't linked correctly
> (on Linux, it usually means Python wasn't even included).  One way to tell
> is to look on the toolbar in Coot - if it doesn't have a button that says
> "Connected to PHENIX" (or something like that), my extension module failed.
>  Which version are you using?  I believe the most recent binary on Bill
> Scott's page may have this problem, but I'll double-check.  I use Fink (
> http://www.finkproject.org/) to install and update Coot, and this has always
> worked quite well as long as Fink doesn't crash on me.
> Also, I noticed that when you run coot from the gui link on MacOS that after
>> manipulating the structure for rebuilding, etc it will freeze requiring a
>> force quit of x-windows to recover. However, if I open coot directly from my
>> xterm on MacOS it works fine and no freezes.  Just a note. Love the program!
> This I haven't heard before.  We have to tamper with the environment
> variables to get Coot to launch from inside Phenix, at least on Linux, and
> this may have side effects.  Where does the console output from Coot end?
> thanks,
> Nat
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

The root of this problem is that I fundamentally don't understand how this works.  But just as a bit of background, I use fink to build the "stand-alone" coot.  The only difference is that I build it in a different directory.  So I would hope that if the fink version works, so should this, but apart from seeing the button appear, I really don't know how to test it.

/sw/bin/coot (or the equivalent) is actually a wrapper script.

The contents look like this:

#!/bin/sh -f 
export COOT_REFMAC_LIB_DIR=/sw/share/coot/lib
export COOT_PYTHON_DIR=/sw/share/coot/python
export PYTHONPATH=/sw/lib/python2.6/site-packages:/sw/lib/python2.6/site-packages/gtk-2.0:/sw/share/coot/python:$PYTHONPATH
/sw/bin/coot-real "$@" 

I suspect PYTHONPATH needs more stuff in it.  What is there is what is required for coot to find its X-windows-based python GUI dependencies.

Could you try replacing the penultimate line with this and see if it works?

export PYTHONPATH=$(dirname $PHENIX_BIN)/base/Python.framework/Versions/2.6/lib/python2.6:/sw/lib/python2.6/site-packages:/sw/lib/python2.6/site-packages/gtk-2.0:/sw/share/coot/python:$PYTHONPATH

If there is a better way, please let me know and I will try to fix it.

Also, what is a good way to test this (keeping in mind that I am basically too stupid to operate the gui)?



More information about the phenixbb mailing list