[chimera-dev] Chimera dumps core on this PDB file

[Eric Pettersen]

This is fixed now and will be in the next (post-1602) release.

--Eric

On Wednesday, September 11, 2002, at 02:38 PM, David E. Konerding wrote:

> 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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