Re: [phenixbb] Phenix and COOT Together on a Mac (and Probe too?)
Nat, One thing that seemed to solve all the problems at once was to completely remove any reference to the COOT path in the Phenix preferences! Is that weird? When I removed it completely only leaving the path to PYMOL then COOT is working just fine in conjunction with Phenix and even the Probe issues have disappeared. Prior to this, I was tried two different paths to COOT. 1. /sw64/bin/coot 2. /Applications/coot.app/Contents/MacOS/coot Neither behaved but if I don't specify anything it works. 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 Tue, Aug 31, 2010 at 12:54 PM, Joseph Noel
One thing that seemed to solve all the problems at once was to completely remove any reference to the COOT path in the Phenix preferences! Is that weird? When I removed it completely only leaving the path to PYMOL then COOT is working just fine in conjunction with Phenix and even the Probe issues have disappeared. Prior to this, I was tried two different paths to COOT. 1. /sw64/bin/coot
This in theory should work, but there is at least one way for it to break (involving a mixup between 32-bit and 64-bit Python modules and Fink vs. system Python). I suspect that is what is breaking on your system.
2. /Applications/coot.app/Contents/MacOS/coot
If you got the app bundle from the CCP4 homepage this will definitely not work, unfortunately - command-line arguments don't get passed to Coot itself.
Neither behaved but if I don't specify anything it works.
Type "phenix.find_coot_command" to see exactly what it's using - on my system, this is /usr/local/bin/coot. -Nat
participants (2)
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Joseph Noel -
Nathaniel Echols