Re: [phenixbb] coot links on Mac

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

On Thu, Jul 29, 2010 at 1:26 PM, Joseph Noel wrote:

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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

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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 [email protected] 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)? Thanks. Bill