[Chimera-users] Chimera 1.1951 on OSX 10.3.4 fails to do much at all...
re: Chimera 1.1951 on OSX 10.3.4 fails to do much at all... I'm a first time user obviously! :-) Trying to open Side View or any of the Tools:Viewing Preferences fails. Many commands via the command interface likewise fail, e.g. surface #0 (no module msms), (no module webrowser). AFAICS from the error messages, the errors appear to be either Python modules missing or Tcl/TK errors. My download is the correct size. Q: Does Chimera require a Tcl/TK installation? - which doesn't show these up and they aren't hidden in one of the sbin's (I'm assuming that they are named tcl and tk - I've never had to work with them directly myself). If so is this tested on start up? There appears to be nothing about this in the docs AFAICS. The OSX installation instructions only say to drag the app. to the disk, nothing about other requirements. So naturally that's all I've done so far! If it does require more stuff, would someone be so kind as to tell me exactly what and where to get it? Two suggestions: It'd be good to have a simple test of what modules are present to "verify" an installation. (e.g. Tools:test:modules) It'd be good to have a test of the presence of Tcl/TK & let the user know it its not around. Grant E.g. of traceback: ImportError: No module named Lighting.controller (see reply log for Python traceback info) Traceback (most recent call last): File "/Applications/Science/Chimera-1.1951.app/Contents/Resources/share/__main__.py", line 56, in ? File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/share/chimeraInit.py", line 301, in init File "tkgui.py", line 2891, in eventLoop File "/usr/local/src/staff/chimera-build/Darwin-X11/foreign/Python-2.3.2/lib/python2.3/lib-tk/Tkinter.py", line 965, in mainloop File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__ File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ File "base.py", line 434, in activate File "base.py", line 80, in menuActivate File "ChimeraExtension.py", line 20, in activate File "base.py", line 102, in module ImportError: No module named Lighting.controller AttributeError: ViewerDialog instance has no attribute 'nb' (see reply log for Python traceback info) Traceback (most recent call last): File "/Applications/Science/Chimera-1.1951.app/Contents/Resources/share/__main__.py", line 56, in ? File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/share/chimeraInit.py", line 301, in init File "tkgui.py", line 2891, in eventLoop File "/usr/local/src/staff/chimera-build/Darwin-X11/foreign/Python-2.3.2/lib/python2.3/lib-tk/Tkinter.py", line 965, in mainloop File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__ File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror File "/private/automount/usr/local/src/staff/chimera-build/Darwin-X11/install/Chimera.app/Contents/Resources/lib/python2.3/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ File "base.py", line 495, in activate File "base.py", line 80, in menuActivate File "StdTools.py", line 81, in activate File "StdTools.py", line 206, in raiseViewingTab AttributeError: ViewerDialog instance has no attribute 'nb' -- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 25 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents.
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
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
-- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 25 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents.
(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
-- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 25 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com
The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. 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.
While I'm writing, I presume Chimera insists on using its own version of python over anything installed in /usr/bin/python or whatever?
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. Eric Pettersen UCSF Computer Graphics Lab
Let me know if you'd prefer we take this offlist so we don't bore anyone else :-) Comments in-line, below. Grant
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 whatever?
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 -- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 25 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training Check out the website for more details: http://www.bioinfotools.com The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents.
participants (4)
-
Eric Pettersen -
Grant Jacobs -
Greg Couch -
Thomas Goddard