[phenixbb] Phenix and COOT Together on a Mac (and Probe too?)

Joseph Noel noel at salk.edu
Mon Aug 30 16:14:18 PDT 2010

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.


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: noel at salk.edu

Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
Web Site (HHMI): http://hhmi.org/research/investigators/noel.html

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