Phenix and COOT Together on a Mac (and Probe too?)
Hi All, 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. I suspect there may be something additional I need to set up to get the two programs to talk to one and other. I can open COOT with the GUI link in Phenix but that's it. The two do not communicate and the "Phenix button" does not appear. I am running everything on a Mac laptop with an Intel chip and the latest snow leopard operating system. 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. Finally, if I do run COOT by starting it from the Phenix GUI it also freezes after several rounds of building, etc just like the probes to check for clashes. If anyone has observed this behavior and has some suggestions I would much appreciate it! Its not a big deal as I can run things separately and work from a print out of Molprobity outliers but it would be sure nice to just click and correct. Sorry to keep going but I should say I have Bill Scott's fink'ed version of coot installed in as directed in /sw64 and the stand alone version installed along with CCP4 and Phenix in my Mac's /Applications directory where all my standard Mac apps appear. Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
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
participants (2)
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Joseph Noel -
Nathaniel Echols