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.
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