- Chimera-dev - RBVI Mailing Lists

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 19 Mar '03

19 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 19 Mar '03

19 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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Re: [chimera-dev] provisional release notes on the web
by Greg Couch 14 Mar '03

14 Mar '03

Maybe the Aqua bugs need to be on a separate web page. Or maybe it is time to give each release its own web page. Any objections to the latter? Greg On Fri, 14 Mar 2003, Thomas Goddard wrote: > I am compiling a long list of Aqua Tk bugs > that afflict Chimera that I will put in the release notes. It will > probably be a couple pages long.

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provisional release notes on the web
by Greg Couch 14 Mar '03

14 Mar '03

Please check out http://www.cgl.ucsf.edu/chimera/docs/relnotes.html and email me any ommisions, clarifications, etc. I believe the bold convention is that it should match capitalized menu entries. Thanks, Greg

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PPC Linux...
by Geoffrey H Wathen 07 Mar '03

07 Mar '03

Is there any chance that a set of PPC Linux binaries will be available at some point? Other than that, my hat's off to you. So far this seems to be an immensely impressive piece of software. Oh, one other thing. Is there a source of pdb files that can be downloaded to provide building blocks for more complex packages? Thank you. Geoff.

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chimera crashes on OSX
by Tom Ferrin 01 Mar '03

01 Mar '03

[ Message content removed at request of tef ]

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registering new file types for chimera
by Greg Couch 28 Feb '03

28 Feb '03

I've added an optional extra argument to chimera.fileInfo.register() that is a list of mime types that correspond to the file type. Feel free to modify your extensions to supply the extra information :-) This will eventually be used by web browsers to invoke chimera. Greg

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Profec
by Michael Trieb 18 Feb '03

18 Feb '03

Dear Chimera developers We have a question concerning the possibility to read files from PROFEC (wich is implemented in Amber 7). We know that this is possible with Midas Plus. We would like to know if this is also possible with Chimera. Thanks in advance Michael Trieb -- Mag. Michael Trieb Universität Innsbruck Institut für Allgemeine, Anorganische und Theoretische Chemie Innrain 52a A-6020 Innsbruck e-mail: michael.trieb(a)uibk.ac.at Tel.: +43(0)512/507-5142

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Re: [chimera-dev] Re: DelPhi in Chimera
by Elaine Meng 17 Feb '03

17 Feb '03

I just wanted to add that if you set the Delphi calculation parameters to also create a Grasp surface, and then use the Grasp surface for display in DelphiViewer, the neutral parts are opaque white. This is true at least in version 1602 and a few preceding versions. In the next release, you can control the color and opacity levels for positive, neutral, and negative potentials explicitly. 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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Re: DelPhi in Chimera
by Thomas Goddard 15 Feb '03

15 Feb '03

Hi Wade DelphiViewer shows positive potentials above the cutoff as blue, negative potentials beyond the cutoff as red, and intermediate values as whi

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ordering in file browser
by Eric Pettersen 13 Feb '03

13 Feb '03

David sent me a mail saying he would prefer the Chimera file browsing widget to separate directories from files in each column, directories first. I am fine with adding this behavior. The question is whether I should allow both the old and new behavior via a preference? I guess I'm polling to see who would prefer the separate files/directories vs. the current purely-alphabetical sorting. Then I can decide whether to keep both behaviors and if I do, which one should be the default. Thanks for your participation! --Eric

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Benchmark correction
by Rey Banatao 10 Feb '03

10 Feb '03

OOPs.... that should read 1GHz not 1MHz processor :) Hey guys- Didn't see specs for the new powerbooks up.... so here ya go. Machine info: Apple Powerbook G4, 1Mhz, 1GB SDRAM, ATI Mobility Radeon 9000 64MB DDR SDRAM running OS X 10.2.3, using Apple's X11 beta (XFree86 4.2.1) Chimera beta Build 1602 Results: surface: 98 mesh: 98 contour: 53 solid: 227 recolor:64

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benchmark
by Rey Banatao 10 Feb '03

10 Feb '03

Hey guys- Didn't see specs for the new powerbooks up.... so here ya go. Machine info: Apple Powerbook G4, 1Mhz, 1GB SDRAM, ATI Mobility Radeon 9000 64MB DDR SDRAM running OS X 10.2.3, using Apple's X11 beta (XFree86 4.2.1) Chimera beta Build 1602 Results: surface: 98 mesh: 98 contour: 53 solid: 227 recolor:64

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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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need your help
by Johannes Fuerst 21 Jan '03

21 Jan '03

Hi there, we are manually fitting crystal structures of proteins into cryo-EM maps with Chimera. Is there a way to read out the coordinates of the fitted crystal structure into a new pdb file, which could then be used for further refinement in other programs (ESSENS or Xplor) Thanx for your help Johannnes Furst Department of Biochemistry Brandeis University 415 South St Waltham, MA 02453

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Re: Chimera issues
by Eric Pettersen 15 Jan '03

15 Jan '03

Hi Slaton, Your list of bugs is very useful and we're kind of abashed that you've encountered so many fatal errors in the 1602 release. I've provided some preliminary comments on your list below. I'll be breaking your list into separate bug reports for entry into our bug-tracking system, so you will be getting several automated mails from that system as they are entered. > Some possible Chimera stability issues/bugs, most experienced using the > Midas Emulator. > > 1. After running conic on a PDB structure, the output image is placed > against a glaring (#f00) red background. When you click on the image to > revert back to standard rendering, Chimera segfaults. Reproduced this on our Linux system. On the SGI, the image was the same, but no seg fault. On a DEC, everything worked right. > 2. Running neon results in the message "/usr/local/midas/bin/neon: > Command > not found." Chimera then segfaults. In the 1602 release we switched from assuming that neon was part of a previous MidasPlus installation to providing it with Chimera. The emulator code wasn't properly updated to reflect this for neon (just conic). The seg fault is a separate problem with the underlying C++ code when the subprogram being run (neon) doesn't exist). > 3. Running ribbonjr results in the message > "/usr/local/midas/bin/ribbonjr: > Command not found." Chimera then segfaults. Ribbonjr isn't supplied with Chimera (only MidasPlus). We expect Chimera's built-in ribbon capabilities to be a sufficient replacement soon and therefore won't be expending the resources to port ribbonjr to the various platforms we support. The seg fault is the same thing as with neon. > 4. If I generate a surface rendering of a PDB structure, and then > adjust > the probe size to very low resolution (say 30A) it segfaults. This is > an > important feature for looking at docking possibilities for smaller > atomic > structures with large low-resolution volumes. Maybe there is a better > way > to "filter" a surface generated from PDB atomic structure to a lower > resolution? Thanks for any advice here. Reproducible. Haven't investigated beyond that. One of our programmers, Tom Goddard, is working on a "multi-scale" extension that will be able to produce low-resolution surfaces of large structures. He might have some advice (he's cc'ed on this mail). We anticipate the initial version of the multi-scale extension will be part of the next Chimera release, which will probably be in March. > 5. If I alt-tab away to another program while surface rendering (of > PDB, > not a volume) is present, when I tab back it segfaults. Haven't reproduced this yet, but only tried on Mandrake Linux. Will try to access a Red Hat box to try it on. > 6. Question, is there any plan to add raytracing ability for producing > publication quality images? Not directly. We anticipate generating input files for popular ray-tracing programs, which you would then run separately. _Might_ be in the next release, though I would guess the release or two after that is more likely. > If not is the best option for this to export > to large TIFFs and reduce size in photoshop/gimp? thanks. Creating a tiff is certainly the current most viable option. The "Save Image" panel is somewhat confusing in this regard, but you shouldn't have to "reduce size" in an external program. You should be able to specify your desired final size in the panel, and use the "Page Setup" button to increase the resolution (in particular, changing the "shades per color" from 2 to 256 will make the numbers in "dots per unit" corresponding 1-to-1 with pixels in the tiff (i.e. if your "units" is inches and "dots per unit" is 400, then the tiff will have 400 pixels per inch). > This is under linux, have tried both red hat 7.3 and red hat 8.0 > releases > on two different dual Xeon systems. One has a GeForce 4 card and the > other > has mediocre onboard ATI Rage graphics. The GF4 card has surprisingly > "blah" performance in Chimera, not poor but not particularly great. > > This is Chimera build 1602. The PDB structure used was 1aoi. > > hope this is useful, > slaton > > Slaton Lipscomb > Nogales Lab, UC Berkeley > http://cryoem.berkeley.edu

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Question: pyhton back log & open gl
by manish 14 Jan '03

14 Jan '03

Visit this UCSF Computer Graphics Laboratory message (to reply or unsubscribe) at: http://www.cgl.ucsf.edu/HyperNews/get/chimeraAlphaTest/10.html Thx very much for availing chimera beta version 1 build 1602. I have absolutely no problems in opening pdb files. I am interested in using extension like dock, molecular dynamics. I hope these extension work freely. Can anyone tell me how to see python back log (when i commit some error I am asked to see the python back log). Regarding, collatory hub, I have a lan connection & I have failed to connect (several times). I have opengl with me but i have not made path for it, I mean autoexec.bat (ms dos) which way i should set the path? could u just type the line. Since my wordstar is not working i am not able to install many programs (autoexec.bat) if anyone can send me 2 lines of installation of babel autoexec.bat I would be thankful to him my config--- celeron 500 mhz windows 98 ------------------------------------------------------------- Visit this UCSF Computer Graphics Laboratory message (to reply or unsubscribe) at: http://www.cgl.ucsf.edu/HyperNews/get/chimeraAlphaTest/10.html

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how can i get "Chimera"
by Joseph Schmoe 11 Jan '03

11 Jan '03

is there a place to register to get "Chimera"? when i goto the download page it asks me to login...i don't have a login. i'd be using the program at home. Dale Carpenter in reference to: http://www.cgl.ucsf.edu/chimera/

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FYI
by Greg Couch 08 Jan '03

08 Jan '03

I've squashed a reference counting bug in our hand-generated conversion code from Python sequences of object to C++ vectors. This mostly affected _chimera::OpenModels:: add and remove, but was also found in the _surfnet code. The memory leaked contained Python class instances and not the associated C++ objects so the effect should have been small.... Greg

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python 2.3
by Eric Pettersen 03 Jan '03

03 Jan '03

Python 2.3 (when we eventually get Chimera using it) has one feature that I think people are going yo want to use: Universal newlines - files opened for reading with the special mode "U" (instead of "r") translate all three commonly found line ending conventions (\n, \r, \r\n) into Python's standard \n convention. Contributed by Jack Jansen. --Eric

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Chimera and Dock
by Eckhart Guthöhrlein 19 Dec '02

19 Dec '02

Hello, our institution was planning to order a copy of MidasPlus, but now we have been told about chimera. A crucial question is: does chimera also include a version of the ms molecular surface calculation program which is suitable for input file preparation for the program DOCK, as it is true for MidasPlus? I could not find the answer in the chimera information available on the web, but I hope that you can help me. Thank you in advance, Eckhart Guthöhrlein

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