[Chimera-users] Chimera 1.1951 on OSX 10.3.4 fails to do much at all...
gregc at cgl.ucsf.edu
Sat Jun 19 09:59:12 PDT 2004
(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).
On Sat, 19 Jun 2004, Grant Jacobs wrote:
> Date: Sat, 19 Jun 2004 16:51:50 +1200
> From: Grant Jacobs <gjacobs at bioinfotools.com>
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Chimera 1.1951 on OSX 10.3.4 fails to do much at
> 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.)
>> 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
>> 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.
> Grant Jacobs Ph.D. BioinfoTools
> ph. +64 3 478 0095 (office, after 10am) PO Box 6129,
> or +64 25 601 5917 (mobile) Dunedin,
> gjacobs at bioinfotools.com NEW ZEALAND.
> Bioinformatics tools: deriving knowledge from biological data
> Bioinformatics tools - software development - consulting - training
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