[Chimera-users] Chimera 1.1951 on OSX 10.3.4 fails to do much at all...

Grant Jacobs gjacobs at bioinfotools.com
Sun Jun 20 15:16:35 PDT 2004

Let me know if you'd prefer we take this offlist so we don't bore 
anyone else :-)

Comments in-line, below.


>On Jun 18, 2004, at 9:51 PM, Grant Jacobs wrote:
>>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 :-)
>AFAIK, Chimera isn't normally location dependent.  On my OS X 10.3.4 
>system at home, I can launch Chimera from the desktop, from my 
>Documents folder, and from /Applications/Science (while named 
>Chimera-1.1951 -- to test your exact situation as closely as 
>possible) and was able to open models and the side view in each case 
>without problem.

Hmm. The only thing I did to get it going was to move 
/Applications/Science/Chimera to /Applications, so that I got 
/Applications/Chimera. Just realised I never moved Chimera-1.1951 
itself right to /Applications; I moved the directory holding it - I 
quite forgot that /Chimera was my doing and not part of the 
installation! So I'll have to stand corrected on that. But the 
strange thing is that moving it did make it work and you'd really 
think this would have no effect. Maybe something completely unrelated 
is going on? Or I'm just having a bizzare week ;-)

Moving /Applications/Chimera back to /Applications/Science/Chimera 
works now. Which is annoying in sense as I can't reproduce the 
original bug. It certainly didn't work on the initial installation.

>Since you have found a solution that works for you, you may not want 
>to pursue this any further.  If you are willing however, you could 
>create a guest account on your machine for our debugging use and 
>convey the account name, password, and machine name to us privately. 
>Then we could debug the problem without requiring much more of your 
>time.  Let us know.

I'd rather not open up my machine. If you want me to do some basic 
things, just let me know. I'd normally have more time, but I've just 
a month before heading to Europe on a round of "let see who might 
support my work" ;-)

I'll try re-installing a copy later tonight (fortunately I keep all 
my installers) and do a little playing around for a few minutes.

>>While I'm writing, I presume Chimera insists on using its own 
>>version of python over anything installed in /usr/bin/python or 
>Pretty much.  Several versions back, the Chimera installer would 
>give you the option of having Chimera use the system version of 
>Python -- but we found compatibility issues were just too much of a 
>headache for both us and users to deal with, so the option isn't 
>there anymore.

I can imagine.

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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