[Chimera-users] occupancy with pdb trajectory

Andrea C. Vaiana vaiana at lanl.gov
Mon Dec 3 19:51:11 PST 2007

Hello everyone,

I am trying to calculate water occupancies from a pdb trajectory. The 
trajectory was generated with gromacs and loaded correctly in Chimera. I 
load the trajectory and it looks fine, I select the water molecules but 
I get this error log (below) when issuing the "calculate occupancy" 
command. Any clues as to what's wrong? I have osx 10.411 on a dual core 
mac book pro running Chimera 1.2470.
BTW I also wasn't able to directly load the gromacs trajectory (tpr and 
trr), the bonds were all messed up from the third frame on.

Any help would be appreciated


AttributeError Exception in Tk callback
  Function: <function command at 0x14757ab0> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
line 1747, in __call__
    return apply(self.func, args)
line 238, in command
    getattr(s, buttonFuncName(txt))()
line 452, in OK
line 105, in Apply
    volumeName=name+" ["+atomType+"]")
"/Applications/Chimera.app/Contents/Resources/share/Movie/gui.py", line 
356, in computeVolume
    self.model.LoadFrame(fn, makeCurrent=False)
line 94, in LoadFrame
    crds = self._ensemble[frame]
AttributeError: PdbTraj instance has no attribute '__getitem__'


Andrea C. Vaiana
Theoretical Biology and Biophysics
Mail stop K710, T-10
Los Alamos, NM 87545
Los Alamos National Laboratory

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