On Mon, Aug 30, 2010 at 4:14 PM, Joseph Noel
I am having trouble getting COOT to link up with Phenix. I know that Bill Scott's fink version of COOT breaks the link but I have also tried the stand alone latest version for Mac OSX without success.
Which stand-alone version? Did you try this one already? http://sage.ucsc.edu/downloads/coot-0.6.2-pre-1-72-64bit.pkg I am using this (also on Snow Leopard) and it has been working great; the only thing I can think to suggest is to make sure that you've set the Coot path to /usr/local/bin/coot in the PHENIX preferences. (This is probably what it will use automatically anyway, but if you have set another path by mistake, or you have multiple Coot installations, it might use the wrong one.) For what it's worth, I've also had good luck with the Fink installation, aside from unrelated flakiness in Fink. On the other hand, I don't do very much model-building. There is one other very remote possibility, which is that you have conflicting Python modules installed. What is the output when you run this command? coot --script $PHENIX/phenix/wxGUI2/Coot.py Usually there is an obvious error message towards the end of the console output. (Actually, if you're starting the GUI from the command line, you may already be getting the same output when you launch Coot.) It might be worth trying this both with /sw64/bin/coot and /usr/local/bin/coot, in case one is more informative.
I can also run probe independently in COOT using the script suggestion for the .coot file from the MOLPROBITY web site. However, after several checks of bad contacts the system freezes at the level of XQuartz and I have to kill X-Windows to start over. I don't know if this is in someway linked to the problem getting COOT and Phenix to talk to one and other but I thought I would throw it out there.
I don't know if this is related, but it sounds like a completely different problem than what we usually encounter - I haven't noticed anything similar. Which version of XQuartz are you using, and what kind of graphics card? -Nat