Thanks Scott. Using your stand-alone Coot package - 0.7 (revision 4459) [with guile 1.8.8 embedded] [with python 2.7.3 embedded], everything works perfectly. The previous issue of "invalid window errors" no longer occurs, and all scripts that use coot now work correctly (as the path /usr/local/bin/coot is defined and understood)
I would tentatively suggest therefore that there are some build issues with the Coot provided as a package from CCP4 - but *weirdly* only when you invoke it from the command line using /Applications/coot.app/Contents/Resources/script - which frequently crashes X11… As a reminder - this was causing me quite a few issues, as other software packages don't expect Coot to live in /Applications - and symbolic linking / path defining wasn't working consistently. NB: Running OS X 10.7.5 (Lion). With regards Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: [email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Dec 6, 2012, at 6:05 AM, William G. Scott wrote: > Dear Tony: > > Any chance you might be willing to try installing from here? > > http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot > > That might give us a positive control (if it works) or help to track down the > problem (if it doesn't). > > It should work the way you want it to. > > Bill > > > William G. Scott > Professor > Department of Chemistry and Biochemistry > and The Center for the Molecular Biology of RNA > 228 Sinsheimer Laboratories > University of California at Santa Cruz > Santa Cruz, California 95064 > USA > Ok - annoying thing…. > > 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from > the command line (terminal window) works IF you don't have X11 open already. > 2) if you DO have X11 open, coot pretty much always crashes with the > aforementioned "invalid window errors". > >>>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: >>>> CGSGetSurfaceBounds >>>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorFailure: Set a >>>> breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >>>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: >>>> CGSBindSurface: Invalid window 0x8da >>>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: >>>> CGSBindSurface: Invalid window 0x8da >>>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: >>>> CGSBindSurface: Invalid window 0x8da > > Ideas and suggestions welcome. I guess I could make sure that X11 is not > running each time I invoke a script or run coot from the command line - but > it's not exactly ideal. > > --> NB: Running Mac OS X, 10.7.5 - Lion.
