April 2003 - Chimera-dev - RBVI Mailing Lists

new Chimera home page
by Tom Ferrin 30 Apr '03

30 Apr '03

The new Chimera home page has gone live, including the new "UCSF Chimera" title logo. Thanks to all that helped on this project. There are still a couple of things left to do, primarily the "latest production version" of the documentation and the "Chimera image gallery" that Dan is working on. But what we have now is a nice improvement from previous version. I plan to use the new images and text as the basis of a printed brochure that Robin is working on. --tom

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Strange behavior, crashing, etc.
by Geoffrey H Wathen 24 Apr '03

24 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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writing multiple PDBs
by Eric Pettersen 22 Apr '03

22 Apr '03

Hi Geoffrey, Writing multiple PDB files via the model panel will be in the next release. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: Chimera for Solaris
by Conrad Huang 15 Apr '03

15 Apr '03

> Could you make a set of binaries for SUN Solaris? Unfortunately, we do not have access to any development Solaris machines, so there is no way for us to test whether our code works on that platform. I'm not even sure whether all the required packages such as OpenGL are standard/available on Solaris. Sorry. Conrad

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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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Chimera-dev April 2003