Strange behavior, crashing, etc.
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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 restarting. 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. Geoff.
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Hi Geoff, Could you send the diamond file that causes Chimera to freeze? I'll check it out. If you don't want that file to be seen by others, send it just to me. In older versions of Mac OS I observed that when the X server crashes the X application icons stay on the Dock even though the application has died. The only way to get rid of them was to restart the Dock. I find the process number and kill it and it restarts automatically. % ps -xw | grep Dock 3402 ?? S 0:06.11 /System/Library/CoreServices/Dock.app/Contents/MacOS/Dock -psn_0_393217 % kill 3402 It may be that you can't restart Chimera after restarting the X server because the Dock thinks Chimera is still running. Restarting the Dock should resolve that. I see that Hide X11 removes the window frames from Chimera windows. That looks like a Tk or Window Manager bug. You can iconify all Chimera windows by just iconifying the main window. After using Hide X11 you can get the dialog frames back by pressing the dialog close buttons and then use the menus to bring back the needed dialogs. Ick. Tom
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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.
Tom Goddard may have already pointed out that using the yellow '-' button will iconize Chimera and hide all it's windows. If you are in the state were you've already hidden X11 and have the title-less windows showing, you can get the title bars back by unhiding X11 and using the yellow '-' button to iconize Chimera (the titleless windows are still there) and then un-iconize Chimera (the windows get their title bars back now). I've put a workaround for this behavior in our current development version and it will be in the next release. If you feel you really need it before then, I can send you instructions as to how to edit the python code (it's a one-line change). Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
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