March 2003 - Chimera-dev - RBVI Mailing Lists

Mac Radeon 9000
by Thomas Goddard 31 Mar '03

31 Mar '03

The Mac system crash with Radeon 9000 graphics have been fixed in a Mac OS 10.2.5 prerelease (build 6L14). The Chimera surface/mesh rendering benchmark scores for the Radeon 9000 were the second highest measured, beat only by the Mac GeForce 4 Ti. I tried rotating large models by hand to check that the benchmark utility is not being fooled. They are correct. As I mentioned before, CPU bound tasks like computing surfaces are significantly slower on the Mac than on x86 hardware. Tom

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Chimera on RH Linux 7.3
by Thomas Goddard 31 Mar '03

31 Mar '03

Hi Jeff, Chimera includes its own version of Tix. When you installed Chimera did you choose to use your system Python? The installer only gives this choice if it thinks your system Python is adequate. But it doesn't do a very thorough test. If you didn't use the Chimera Python you may want to reinstall and use it. If this is not the problem, it would help us to see the strace output when starting Chimera, to see what libraries are being used: % strace chimera Thanks, Tom

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Re: Chimera start-up problem - final word on SuSE8.0
by Thomas Goddard 31 Mar '03

31 Mar '03

Hi Jim, The strace output you sent shows that Chimera is using the system python /usr/bin/python2.2 on your machine. That is loading the system Python Tk module (called Tkinter) and that is linked against Tcl/Tk 8.3 and Tix 8.1 while Chimera requires Tcl/Tk 8.4 and Tix 8.2. The solution here is to reinstall Chimera. I'm guessing that it asked you whether you wanted to use the system Python or the one provided with Chimera, and you elected to use the system Python. You need to use the Python provided Chimera. If the installer does not ask about which Python to use let me know. Tom

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testing new mailing list software
by Conrad Huang 19 Mar '03

19 Mar '03

Please disregard

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Mailing list?
by Geoffrey H Wathen 19 Mar '03

19 Mar '03

Okay, I think this will be the last one tonight, if for no other reason than the fact that I'm about ready to go to bed... Is there any chance that there is or will be a mailing list for Chimera users, so that newbies (like me) can learn from people who are more experienced? I've used other software packages, and this kind of a community is always a big plus. And, yet again, thank you. Geoff.

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Re: [chimera-dev] Docs...
by Elaine Meng 19 Mar '03

19 Mar '03

Hello, Geoff, If you are using the documentation bundled with your release it should match your software (you have to go via the Chimera Help menu). If you are looking at the documentation linked to the Chimera home page, that is always updated with newer things and will not match your current software. That is, the documentation linked to our web site will usually be AHEAD of the software you are using. We have recently found a problem with a few of the tutorial sample input files being missing from the bundled documentation; in those cases, they can be retrieved from the documentation linked to the Chimera web site. These files have not changed, only the associated tutorial text. To summarize, to get the documentation matching the Chimera you are using: start Chimera, choose Help... User's Guide from the menu. The guide should pop up in a browser window. In the few cases where a sample input file is not findable in the bundled tutorial, it can be downloaded from within the updated documentation at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html If anything is unclear, please do contact me (User's Guide documentarian) Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Computer Graphics Lab and Babbitt Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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Docs...
by Geoffrey H Wathen 18 Mar '03

18 Mar '03

Another quick note- Any chance the documentation will be updated anytime soon? I noticed that the current menu structure in Chimera isn't quite the same as that described in the tutorials. This makes it a little harder to learn how to use the application (though I am managing...). It would still be helpful to have updated documentation... Again, thank you. Geoff.

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Mac OS X
by Geoffrey H Wathen 18 Mar '03

18 Mar '03

Just a quick suggestion... I have loaded the beta release of OpenOffice.org for Mac OS X, and it has a launcher similar to the launcher that you have provided for Chimera. Interestingly, their installer has some functionality that yours doesn't, and yours has some that theirs doesn't. Specifically, I'm writing to suggest that you allow your launcher to launch X11 (or whatever X Window implementation the user has installed) before trying to launch Chimera. Right now, it seems that if I don't remember to launch X11 first, I get to see Chimera bounce for a little while, then it just goes away, no error message, or anything. Thanks for your attention. Geoff. P.S. Incidentally, the functionality that you've managed that they don't have is that the Chimera (launcher) icon only stays in the Dock as long as Chimera is running. The OOo launcher has to be quit separately from the OOo application itself.

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residues in highlight lens?
by David E. Konerding 17 Mar '03

17 Mar '03

Hi, from what I can tell, there is no way to use the ribbon representation within the highlight lens; the options are limited to atom and bond representations. I am hoping to turn on only the ribbon representation in the highlight lens, leaving atom and bonds disabled. Is this available? If it isn't, wouldn't this be a reasonable feature to add to the highlight lens? thanks, dave

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specular reflection
by Irina Serysheva 17 Mar '03

17 Mar '03

Hi, I was wondering if there is any way I could change specular reflection settings or turn it off. Thank you. Irina -------------------------------------------------------------- Irina I. Serysheva, Ph.D. National Center for Macromolecular Imaging Department of Mol.Physiology & Biophysics Baylor College of Medicine One Baylor Plaza Houston, TX 77030 Telephone: (713) 798-4261 (office) (713) 798-6989 (EM lab) (713) 798-5720 Fax : (713) 798-3475 E-mail : irinas(a)bcm.tmc.edu http://ncmi.bcm.tmc.edu/~irina

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Chimera-dev March 2003