September 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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[Fwd: [omniORB] ANN: omniORB 4.0.0 and omniORBpy 2.0]
by David Konerding 25 Sep '02

25 Sep '02

Hi, OmniORB 4.0 and OmniORBpy 2.0 have been officially released. They add a number of really nice features of OmniORB and fixed many bugs, (see attachment) and I think the next release of Chimera would benefit from moving to this new version. Dave

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Re: [chimera-dev] duping status in replies
by Eric Pettersen 17 Sep '02

17 Sep '02

On Tuesday, September 17, 2002, at 11:26 AM, Thomas Goddard wrote: > How about log? 'log' seems okay by me. I'll change it this afternoon unless someone objects. --Eric

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duping status in replies
by Eric Pettersen 17 Sep '02

17 Sep '02

Once I had implemented an 'echoToReplies' keyword in ModelessDialog status lines, I immediately became too lazy to not have the same keyword available to replyobj.status(). So now the latter has the keyword also (default false). --Eric

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question about AddH
by Euna Jeong 12 Sep '02

12 Sep '02

Dear Chimera developer, I am looking for a program to add hydrogen atoms to a pdb file. Chimera is a good tool to do it. After adding hydrogen atoms to a PDB file, I'd like to save the result file to a PDB file, not tiff image . Chimera can do that now? Thanks. Euna Jeong School of Computer Science and Engineering Inha University Inchon 402-751, South Korea 82-32-860-7388 (phone) 82-32-863-4386 (fax)

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Re: bad PDB
by David E. Konerding 12 Sep '02

12 Sep '02

Elaine Meng wrote: > Hi Dave, >When I opened it (it did open on the SGI), I got the usual >bad PDB record warnings, plus: >warning: duplicate atom serial number found: 1 >warning: duplicate atom serial number found: 2 >warning: duplicate atom serial number found: 3 >warning: duplicate atom serial number found: 4 >warning: duplicate atom serial number found: 5 >warning: duplicate atom serial number found: 6 >(etc. on up to 141) >Perhaps this is the problem. I deleted the first 141 atoms with 0.0 >coords and did not get those messages; that still leaves plenty of >0.0 coord atoms at the end, which are not complained about. You might >want to try this. >Elaine > > By the way, I fixed the atom serial numbers so they are numbered sequentially from 1, and chimera still crashes, showing it's not related to the serial number warning. Dave

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GUI design
by Greg Couch 10 Sep '02

10 Sep '02

Apple has released its "Aqua Human Interface Guidelines" in both html and pdf formats at: <http://developer.apple.com/techpubs/macosx/Essentials/AquaHIGuidelines/>. Chapter 2 "Human Interface Design Principles" looks good. And the section on "Using Ellipses in Menus and Buttons" might still be useful :-). There is also a short guide for Windows programmers at: <http://developer.apple.com/ue/switch/windows.html>. Greg

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Feature request
by David E. Konerding 10 Sep '02

10 Sep '02

I would like the "sequence panel" to be on the "Controllers menu". Since the sequence panel normally requires a model to be selected first (since it only displays the sequence of 1 model at a time), it should be updated to show sequences for all models. It's very clunky to have to go Controllers->Model Panel->select model->scroll to sequence->click sequence given that dealing with the protein sequence is such a common operation. Dave

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new PC version available internally
by Greg Couch 03 Sep '02

03 Sep '02

on socrates in /usr/tmp/gregc/chimera1.1549.exe. Enjoy. It is already installed on ryle :-) Greg

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Chimera-dev September 2002