November 2002 - Chimera-dev - RBVI Mailing Lists

Chimera dumps core on this PDB file
by David E. Konerding 30 Jan '03

30 Jan '03

Chimera on my Red Hat system, somewhat understandably but not acceptably in my opinion, dumps core on this PDB file. In CASP, if you can't define a part of the model you submit it with coordinates set to 0. I wonder if Chimera is trying to divide by zero (although I would except a SIGFPE, not a segmentation fault). I did a remote-display from socrates and it had the problem as well; there, I at least got a popup window saying "_chimera: unknown exception" and was able to see this in the reply log: Error processing trigger "addModel": _chimera error: can't normalize zero length array (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 56, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 240, in init prefixableType=1) File "/usr/local/chimera/share/chimera/__init__.py", line 628, in open skipViewAll=skipViewAll) File "/usr/local/chimera/share/chimera/__init__.py", line 509, in add self.triggers.activateTrigger(self.ADDMODEL, models) File "/usr/local/chimera/share/chimera/triggerSet.py", line 198, in activateTrigger self._triggerDict[name].activate(data) File "/usr/local/chimera/share/chimera/triggerSet.py", line 120, in activate ret = handler.invoke(self._name, triggerData) File "/usr/local/chimera/share/chimera/triggerSet.py", line 82, in invoke self._funcData, triggerData) File "/usr/local/chimera/share/chimera/__init__.py", line 837, in checkKsdssp model.computeSecondaryStructure(-0.5, 5, 4) _chimera error: can't normalize zero length array shortly after visiting the window a few more times, chimera segfaults. Dave

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About the DMS program in chimera
by Ming Lei 26 Nov '02

26 Nov '02

Dear Sir: I am using the chimera. And I knew it is a updated version of mediaplus. I wonder if there still is dms program to generate the ms input file for docking(SPHEN). If yes, can you tell me how to use it in chimera? Your immediately reply is much appreciated! Best, Ming ___________________________________ Ming Lei Ph.D Postdoctoral Research Associate Department of Chemistry Clark University Worcester, MA 01610 Tel: 1-508-421-3742 (Lab ) 1-508-831-9851 (Apt ) Email: milei(a)clarku.edu

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dms, Chimera
by Elaine Meng 26 Nov '02

26 Nov '02

[I forgot to cc chimera-dev so have enclosed the message to Ming Lei below] Dear Ming, Currently there is no dms program that comes with Chimera. It is something we want to have in the future, however. If you already have MidasPlus, you can continue to use the dms that comes with MidasPlus for making SPHGEN input. Best regards, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., 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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Help
by Srinivasan, Mythily 25 Nov '02

25 Nov '02

Hi, I am using Chimera (Windows 2000) operating system. I have a protein complex with two distinct chains. I would like to find the intersections of groups of atoms between the two chains. As I understand from the tutorials for Midas, the & operator should help me. However, I get a syntax error message. Can you please tell me the correct command? Thanking you, Sincerely, Mythily Indiana University School of Dentistry

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[stevel@blake.3dem.bioch.bcm.tmc.edu: Re: Chimera at NCMI]
by Thomas Goddard 25 Nov '02

25 Nov '02

------- Start of forwarded message ------- Date: Mon, 25 Nov 2002 13:37:43 -0600 (CST) From: Steven Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> X-X-Sender: stevel(a)id.3dem.bioch.bcm.tmc.edu Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.EDU> Subject: Re: Chimera at NCMI In-Reply-To: <200211251932.gAPJWPdN690278(a)adenine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.9 (cgl.ucsf.edu) On Mon, 25 Nov 2002, Thomas Goddard wrote: > I don't understand why the installer failed when installing in > /home/stevel/chimera. I just tried the linux installer from the web > in my home directory and it worked. If it works as root for you, that seems > to indicate it is a permissions problem. Can you send me the permissions > on your home directory, "ls -l /home/stevel"? It should also work if > you create the chimera directory first. I tested that and it also > worked. The installer no longer removes an old Chimera. If you try > to install where a Chimera already exists, it will ask you to move it > or delete it yourself (from another shell) before proceeding. Found the problem. Stupidity on my part (as ususal). One machine uses /homes/stevel, the other uses /home/stevel, and I got them backwards. > I agree that the web page should say next to the download link > the date and version of the last release. Currently you have to > follow the release notes link from the home page to check this. > If you already have Chimera running, the Help/Software Updates > menu entry will tell you if you have the most recent version. Good tip. > The Puppet extension for remote controlling chimera uses the Tcl socket > command to listen for socket connections. When a new connection is made > a Tcl event appears in the event loop. I couldn't get that behaviour with > the Python socket module, and I didn't try a separate thread. Using Tcl > socket worked ok, but I don't know if it handles unix domain sockets. > I was using INET domain sockets and Puppet just checks that the connection > is being made from the machine chimera is running on. That is obviously > inadequate security on a multi-user machine. The Puppet extension is not > distributed with Chimera because of this security problem. I think I gave > you a copy several months ago. If you can't find it, I can provide you > another copy of the Puppet Python code. Yeah, I've still got it. I sort of wanted to avoid doing any explicit TCL stuff. I hadn't checked to see how you handle that. Anyway, that answers my question Thx, and sorry to waste your time on the installer thing... - -- - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds ------- End of forwarded message -------

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Re: Chimera at NCMI
by Thomas Goddard 25 Nov '02

25 Nov '02

Hi Steve, I don't understand why the installer failed when installing in /home/stevel/chimera. I just tried the linux installer from the web in my home directory and it worked. If it works as root for you, that seems to indicate it is a permissions problem. Can you send me the permissions on your home directory, "ls -l /home/stevel"? It should also work if you create the chimera directory first. I tested that and it also worked. The installer no longer removes an old Chimera. If you try to install where a Chimera already exists, it will ask you to move it or delete it yourself (from another shell) before proceeding. I agree that the web page should say next to the download link the date and version of the last release. Currently you have to follow the release notes link from the home page to check this. If you already have Chimera running, the Help/Software Updates menu entry will tell you if you have the most recent version. If chimera is installed as root, users can still add their own directory of extensions using Extensions/Manager/Directories tab. Chimera will definitely remain free for academic users. The Puppet extension for remote controlling chimera uses the Tcl socket command to listen for socket connections. When a new connection is made a Tcl event appears in the event loop. I couldn't get that behaviour with the Python socket module, and I didn't try a separate thread. Using Tcl socket worked ok, but I don't know if it handles unix domain sockets. I was using INET domain sockets and Puppet just checks that the connection is being made from the machine chimera is running on. That is obviously inadequate security on a multi-user machine. The Puppet extension is not distributed with Chimera because of this security problem. I think I gave you a copy several months ago. If you can't find it, I can provide you another copy of the Puppet Python code. Tom

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[stevel@blake.3dem.bioch.bcm.tmc.edu: Chimera at NCMI]
by Thomas Goddard 25 Nov '02

25 Nov '02

Steve Ludke in Wah Chiu's group reports some Chimera problems. He uses Linux. Tom ------- Start of forwarded message ------- Date: Mon, 25 Nov 2002 10:42:39 -0600 (CST) From: Steven Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> X-X-Sender: stevel(a)id.3dem.bioch.bcm.tmc.edu Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.EDU> Subject: Chimera at NCMI In-Reply-To: <200207230235.g6N2ZVWN661878(a)adenine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.9 (cgl.ucsf.edu) Hi again. Well, I've started working on using chimera as a visualization extension for another program and I've got a couple more questions/comments from things I've run into recently. : 1) I just downloaded the latest release, but it fails when I try to install it as non-root with a destination of /home/stevel/chimera (see end). 2) One problem I keep running into is when I go to your web page, I have no way to tell if the version I have is the most recent, or if you've put a new one up. Perhaps you could put an upload date on the webpage. A build number might also not be a bad idea... just a suggestion :^) 3) If chimera is installed as root, is there some way for users to include their own extensions ? 4) Since I'm trying to use chimera as a sort of integral extension to one program, and may increase this usage in future, I just wanted to insure that it's not suddenly going to be a commercial product (for academic users anyway). Is this something I can rely on ? 5) Finally, a technical question. Currently I'm spawning a new thread to handle the interprocess communication (I'm using unix-domain sockets for security at the moment). Anyway, the thread solution has a number of problems, of course, largely due to bugs at the moment. I was considering trying to implement an event-loop function instead, perhaps by registering an idle-event in Tk. Just wondering if there is anything I should be aware of before tackling this approach... Thanks, and I really do appreciate all the work you guys have put into chimera. I really hope that the method I'm working on will work. If so, I should be able to garner a couple of hundred additional users for you :^) - ----------------- id> ./chimera1.exe UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu). extracting: chimera_install_5xJwd7/py2.2.exe extracting: chimera_install_5xJwd7/chimera.exe extracting: chimera_install_5xJwd7/check.py extracting: chimera_install_5xJwd7/installer extracting: chimera_install_5xJwd7/chimera Enter install location [hit enter for default (/usr/local/chimera)]: /home/stevel/chimera /home/stevel/chimera: No such file or directory ERROR in create_install_dir: mkdirhier: failed to make directory ERROR in chimera_final_install: Could not create install dir: '/home/stevel/chimera' result code from installer: 256 Installer returned unexpected return code '256' Cleaning up extract dir, 'chimera_install_5xJwd7' Installation is done; press return. (I tried creating the directory manually too, still fails) - -- - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-6989 | Dept of Biochemistry and Mol. Biol. instant messenger: sludtke42 | * Those who do ARE * http://ncmi.bcm.tmc.edu/~stevel | The converse also holds ------- End of forwarded message -------

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NVidia, Linux, and Stereo tidbit
by Greg Couch 20 Nov '02

20 Nov '02

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Re: Results from Monday's meeting
by Greg Couch 19 Nov '02

19 Nov '02

Part of the solution would be to use a UNIX domain socket on UNIX and a named pipe on Windows with the permissions set so only the user running chimera can send messages to it. Greg On Tue, 19 Nov 2002, Thomas Goddard wrote: > The two main difficulties with Puppet are registering the helper > application with your web browser, and security. The security problem > is that the Chimera side of Puppet listens on a socket and has no way > of verifying that the request comes from the Chimera user. Currently > it accepts connections only from the localhost, but the connection > could come from another user on the machine. It also has a mode where > Chimera will not execute the Python code sent to it until you press a > Run button on the Puppet dialog. That mechanism is too cumbersome for > real use. > > The security problems would have to be solved before the Chimera installer > could attempt to register Puppet with the user's web browser.

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cvs update
by Greg Couch 18 Nov '02

18 Nov '02

A couple of things -- the release branch changes have been merged back in to the main branch (a.k.a., the HEAD branch). So please update all of your cvs checkouts with the -dP flags to delete removed files and add new ones. Some deleted files were creeping back in. Thanks, Greg

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Chimera-dev November 2002