Ok - problem resolved. Would appear to be a problem with X11 on our current system image. Installing Xquartz 2.7.4 (http://xquartz.macosforge.org) and replacing the default X11 from Apple - seems to have cured all ills.
Many thanks to Bill Scott, Nat Echols and Charles Ballard for their off-list help. All installations of Coot - both CCP4 and Bill's now work correctly, whether invoked from the coot.app, via the script, or from the command line. 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 11:12 AM, Antony Oliver wrote: > 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.
