(On the chance that Tom has already left for vacation, and won't be able to reply for a week.) Glad to hear that it works when it's in /Applications. We didn't intend for chimera to be location-dependent, so we'll look into that problem. Chimera includes it's own python and should use it. That's why the Tom's email mentioned the PYTHONHOME, PYTHONPATH, and CHIMERA environment variables -- those should be the only possible way of confusing chimera and if they're not set, then that means that there is a less obvious bug to fix (the non-Mac versions of chimera prevent those environment variables from confusing chimera, and the Mac should too). - Greg On Sat, 19 Jun 2004, Grant Jacobs wrote:
Date: Sat, 19 Jun 2004 16:51:50 +1200 From: Grant Jacobs <gjacobs@bioinfotools.com> To: Thomas Goddard <goddard@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Chimera 1.1951 on OSX 10.3.4 fails to do much at all...
I've tried a few things -- seems Chimera is location-dependent. I place most of my applications in subdirectories of /Applications or ~/Applications (e.g. Text, Graphics, Science, etc.) to organise things a bit. A few apps. insist on being in /Applications - Chimera seems to be one of these. Your installation notes don't indicate this explicitly, but I suppose no many people insist on being so over-organised :-)
While I'm writing, I presume Chimera insists on using its own version of python over anything installed in /usr/bin/python or whatever?
(Just in case you think your reply was of no help, it was the ls example that got me thinking it might be the location.)
Cheers,
Grant
Hi Grant,
Chimera comes with Tcl/Tk and Python and everything that is needed. Either your Chimera installation did not work, or environment variables are tripping up Chimera.
To see if all of Chimera got installed use Mac Finder and single click on Chimera. On my Mac OS 10.3.4 system it says 132.9 Mb disk space is being used by Chimera. Is that what you see?
More likely the problem is with environment variables. Do you have PYTHONHOME set in your environment? If you start a Terminal and type echo $PYTHONHOME it will say if this variable is set. Other environment variables that could mess up Chimera are PYTHONPATH and CHIMERA.
If all of this looks ok try
% ls /Applications/Science/Chimera-1.1951.app/Contents/Resources/share/Lighting
from a Mac Terminal. This is the location of the missing file referenced by the Python error you sent. You should see the following files:
ChimeraExtension.py* controller.py* __init__.py* ChimeraExtension.pyc controller.pyc __init__.pyc
Lastly, we have separate Mac OS 10.2 and 10.3 versions of Chimera on our web site. If you still have the Chimera dmg it should be chimera-1.1951-osx10_3_x11.dmg, not chimera-1.1951-osx_x11.dmg.
Tom
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