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: [log in to unmask]
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.
|