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: [log in to unmask]
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: [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.
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