- Chimera-dev - RBVI Mailing Lists

Chimera for Solaris?
by Gary Williams, Tel 01223 494522 15 Apr '03

15 Apr '03

Could you make a set of binaries for SUN Solaris? Thanks, Gary -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams@hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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case-dependent chain IDs
by Eric Pettersen 08 Apr '03

08 Apr '03

Hi all, David Konerding has pointed out to me that treating chain IDs in a case-independent manner is becoming a problem with the very big structures that are now being deposited. Both 1fnt and 1ml5 have chain IDs that differ only in case. Right now PDBio uppercases chain IDs, so there is no possibility for the rest of Chimera treating them correctly. I guess the question is what do we want to do? We could just stop PDBio uppercasing them. This mostly works, but has the drawback that chain IDs in atom specs now have to be typed in the correct case, which is inconvenient compared to the way it is now where you can just type in all lowercase (which is perfectly fine for 99.99% of structures where there are < 26 chains and the lowercase chain ID is unambiguous). My thinking is that there could be a model-level function that declares whether chain IDs are case-sensitive for that model, and the atom-spec code could query that function do decide how to test chain IDs on a per-model basis. Other than this, I am stumped for a good solution other than making people type the correct case for chain IDs. Opinions? --Eric

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[wathen@physics.arizona.edu: Re: [chimera-dev] Mailing list, etc.?]
by Thomas Goddard 08 Apr '03

08 Apr '03

------- Start of forwarded message ------- Date: Fri, 4 Apr 2003 20:00:09 -0700 Subject: Re: [chimera-dev] Mailing list, etc.? Content-Type: text/plain; charset=US-ASCII; format=flowed From: Geoffrey H Wathen <wathen(a)physics.arizona.edu> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> In-Reply-To: <200303191730.h2JHU1Kh779813(a)adenine.cgl.ucsf.edu> X-Filter-Version: 1.9 (cgl.ucsf.edu) Tom, I've downloaded the latest build of Chimera. It seems as stable as ever, but I do note that you chose to keep with the X server version, rather than going to Aqua. (I also noticed that the launcher now does give the error, informing you that you need to start the X server, if it isn't already running.) Any thoughts on a mailing list, yet? If you'd like to have someone volunteer to be a list moderator, I'd be happy to. (Also happy to help out any other way that I can...) 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.) In any event, thank you for all of your efforts. Geoff. On Wednesday, March 19, 2003, at 10:30 AM, Thomas Goddard wrote: > Hi Geoff, > > We will be making a Chimera release in then next week or two > possibly as early as this Friday. We have been testing an Aqua version > of Chimera (no X server needed) but have encountered about a dozen > problems with the Tk windowing toolkit on Aqua that Chimera uses. > We are still considering whether to release an Aqua version or an > X windows version. > > If we decide to continue with an X windows Chimera on the Mac then > I will look into how OpenOffice starts the X server if it is not > yet started. I agree that the current Mac Chimera behaviour where > no error is shown when you don't first start the X server is bad. > > The tutorials on our web site describe our development version of > Chimera that has not been released. We may have it up on the web > because > people at UCSF have access to that newer Chimera. I'll see if we can > keep the current Chimera release manuals on the web. Your Chimera > distribution came with the manuals and tutorials. If you go to the > Chimera Help menu and select User's Guide the web browser will show > the copy that came with your Chimera distribution which should be > completely consistent (same menus, ...) with that version of Chimera. > > We do not have a Chimera mailing list. This next release is > the first official release (may still be a beta release on the Mac > platform) > and it makes sense to look into setting up a mailing list. > > Tom > ------- End of forwarded message -------

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writing multiple PDBs
by Elaine Meng 07 Apr '03

07 Apr '03

Hi Geoff, If the main reason you want to write multiple PDBs to a file is to preserve their relative orientations, you can essentially do that with "write PDB" successive times on different models but always relative to the same model. I concede that could be tedious, however. Pdbrun cat is a little dicey since you need to make sure all the atoms you care about are displayed, since only those will be included. Also, with multiple models, I think it puts an END record in between, which needs to be removed if you are going to reopen the file and display the models. As you probably noticed, a lot of USER records get included in the file unless you use the keyword nouser. Hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, Ph.D. Babbitt Lab and Computer Graphics Lab meng(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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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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