January 2003 - 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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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 13 Jan '03

13 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 10 Jan '03

10 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 07 Jan '03

07 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-dev January 2003