[Chimera-users] Auto start and nogui option causing segmentation fault?

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 25 10:28:30 PDT 2016


Hi Daniel,
Hmm, I’m not aware of other startup options to prevent such errors in nogui mode.  It may simply be necessary to use a different preferences file ( you can have multiple ones and specify the one to use with the —preferences startup option ) without autostarts for running Chimera in nogui mode.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html>

You could report this as a bug  with Help… Report a Bug in the menu (GUI version, of course) or the address chimera-bugs at cgl.ucsf.edu .  Even though the problem seems to be with the nogui version, the menu approach is useful because it automatically includes Chimera version and platform information.  Either way, you could just paste in what you wrote in this message.  Since I’m no help in this case, reporting a bug is good to make sure that the right people see it (although some are currently away, so it may be few days before there is any response), and to get it into our bug-tracking system.

Sorry for the inconvenience,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 21, 2016, at 12:44 PM, Daniel P Farrell <danpf at uw.edu> wrote:
> 
> Hello,
> 
> I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode. 
> 
> I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui.  Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway.  Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options.
> 
> chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC
> 
> with many auto-start options on
> """
> >chimera --nogui
> Exception in Tkinter callback
> Traceback (most recent call last):
>   File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__
>     return self.func(*args)
>   File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit
>     func(*args)
>   File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck
>     if not preferences.get(GENERAL, DIALOG_PLACEMENT):
>   File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get
>     return self._category[category].get(name,
> KeyError: 'General'
> [1]    1045 segmentation fault  ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui
> """
> after removing most auto-start options
> """
> >chimera --nogui
> Exception in Tkinter callback
> Traceback (most recent call last):
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__
>     return self.func(*args)
>   File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit
>     func(*args)
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck
>     if not preferences.get(GENERAL, DIALOG_PLACEMENT):
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get
>     return self._category[category].get(name,
> KeyError: 'General'
> Starting extension 'Model Panel' failed
> 
> Starting extension 'Keyboard Shortcuts' failed
> 
> Starting extension 'IDLE' failed
> 
> >
> 
> """
> should I be adding a different flag or something when I start chimera via nogui?
> 
> Thanks,
> Dan




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