[Chimera-users] Strange behavior, crashing, etc.

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Thu Apr 24 11:32:44 PDT 2003

Okay, Chimera has rather suddenly gone unstable on me.  I can fully 
appreciate that it might be something that I've done, but I'd like some 
help getting it usable again.  I've seen two different behaviors now.  
The first is that when I load a pdb file of a calcite crystal, then try 
to rotate the crystal... boom.  Chimera crashes and everything is gone.
	I'm not sure if this has to do with this one file or not.  In an 
attempt to figure that out, I relaunched Chimera and started opening 
files, one at a time.  The first file, a small NaCl crystal, opened 
just fine.  I could rotate it, etc.  I closed it, and opened a file 
with graphite in it.  Same thing, everything was fine.  Next I opened a 
diamond file.  This turns out to have been a big mistake.
	When I tried to open the diamond file, everything froze.  I couldn't 
close any of the Chimera windows or pallets.  None of the menus would 
respond.  After waiting for a little bit, I quit X11.  This 
successfully shut Chimera down, but there's now a new problem.
	When I quit X11, the Chimera icon stayed in my dock.  Right clicking 
on it brings up the contextual menu saying that the application is not 
responding, but choosing 'Quit' from this menu does nothing, and 
Chimera doesn't show up in the Force Quit dialog.  To top it all off, 
relaunching X11, and then double clicking on Chimera (the application, 
not the dock icon) does nothing.  Chimera seems to be down for the 
count.  I haven't yet tried a command-line 'kill process', or 
	The only two major changes/additions that I've made to my computer 
recently are updating to Mac OS X 10.2.5, and installing Fink.

	On a rather unrelated note, Chimera behaves very strangely if you Hide 
X11 while Chimera is running.  All of the pallets simply have their 
title bars vanish, making it very difficult to work with them.  I've 
gotten past this by using multiple desktops, but being able to hide an 
application while working in another is a valuable feature, and I'd 
like to see the proper functionality established, if that's possible.


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