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

David E. Konerding dakone at uclink.berkeley.edu
Wed Sep 11 14:38:36 PDT 2002

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
  File "/usr/local/chimera/share/chimera/__init__.py", line 628, in open
  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 
  File "/usr/local/chimera/share/chimera/triggerSet.py", line 120, in 
    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 
    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.


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