April 2003 - Chimera-users - RBVI Mailing Lists

Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 25 Apr '03

25 Apr '03

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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Re: [chimera-dev] Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Hi Geoff, Eric Pettersen tells me Chimera is hanging when you display diamond.pdb in ball and stick or sphere mode because it is searching for rings. There are too many rings to find. Eric will look at fixing the ring finding code. The reason it needs to know the rings for some display modes is so it can identify atom types (classed by connectivity) so it can assign correct atom radii. You can work around the problem by issuing a Chimera command to set the vdw radii before using ball and stick or sphere display. Use Favorites/Command Line and type a command like vdwdefine * * 1.0 This example sets all atom radii to 1 angstrom (for sphere display). See the User's Guide under Commands for details on setting the radii of specific atoms if you want different atoms shown with different sizes. Any application, Aqua or not, can have an icon in the Dock -- it just has to be packaged with the Mac App directory layout and have an icon file. But Force Quit apparently only lists Aqua applications. The Aqua version of Chimera is shown in the Force Quit list. Tom

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Re: [chimera-dev] Strange behavior, crashing, etc.
by chimera-users＠cgl.ucsf.edu 24 Apr '03

24 Apr '03

Hi Geoff, Chimera freezes up for me after I open diamond.pdb and then try to show it as ball and stick or sphere. It doesn't freeze up with wire display style. When it freezes I use: % ps -xwww | grep python2.2 3676 ?? R 0:44.37 /Users/goddard/Applications/Chimera-X11-1700.app/Contents/Resources/bin/python2.2 /Users/goddard/Applications/Chimera-X11-1700.app/Contents/Resources/share/__main__.pyp % kill 3676 The Chimera executable is python2.2 and this just kills Chimera, not the X server. It doesn't appear in the Force Quit dialog because it is not a native Aqua windows application. Are you using Chimera build 1700 (March 27, 2003)? The Chimera Help/Version Info menu entry will tell you which version you have. I'll look into why Chimera 1700 is freezing on diamond.pdb. Tom

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Re: [chimera-dev] Mailing list, etc.?
by chimera-users＠cgl.ucsf.edu 08 Apr '03

08 Apr '03

> Now to a comment. After some tinkering, I finally managed to output a > new PDB file that contained models from several other PDB files. This, > however, wasn't exactly an easy of intuitive thing to do. My first > thought had been to use the 'Write PDB' command in the Model Panel. > However, that button automatically greys itself out when more than one > model is selected. I finally stumbled upon the command line command > 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to > go through a rather backdoor method. Any chance that things like > 'Write PDB' will be enabled when more than one model is selected? I could enable 'write PDB' with multiple models selected. I guess my question is why do you want multiple PDB models in a single file? What will you do with that file? Knowing how you want to use the file will help me decide if simply enabling the button is the way to go or if some other interface is more appropriate. If I enabled it, the models would be separated by END records. > And what about a method of adding more atoms, other than just > hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd > love to see Chimera become a more fully featured molecular modeler, and > to that end, I'm quite happy to give all kinds of input.) I'm currently working on smarter hydrogen addition (avoiding steric conflicts and maintaining hydrogen-bonding interactions). I should be done with that in time for our next release. I intend to work on some limited structure-building features after that. So a preliminary version might be available two releases from now. Even I'm not aware of backdoor ways to add non-hydrogen atoms! I guess the swapaa command _sort_ of does this, but it's not at all generic. Are you writing Python code to do this? Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [chimera-dev] Mailing list, etc.?
by chimera-users＠cgl.ucsf.edu 07 Apr '03

07 Apr '03

On Monday, April 7, 2003, at 10:06 AM, Thomas Goddard wrote: > Now to a comment. After some tinkering, I finally managed to output a > new PDB file that contained models from several other PDB files. This, > however, wasn't exactly an easy of intuitive thing to do. My first > thought had been to use the 'Write PDB' command in the Model Panel. > However, that button automatically greys itself out when more than one > model is selected. I finally stumbled upon the command line command > 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to > go through a rather backdoor method. Any chance that things like > 'Write PDB' will be enabled when more than one model is selected? > And what about a method of adding more atoms, other than just > hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd > love to see Chimera become a more fully featured molecular modeler, and > to that end, I'm quite happy to give all kinds of input.)

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Chimera-users April 2003