On Dec 3, 2007, at 7:51 PM, Andrea C. Vaiana wrote:
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
Regards,
Andrea
AttributeError Exception in Tk callback
Function: <function command at 0x14757ab0> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File
"/Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File
"/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",
line 238, in command
getattr(s, buttonFuncName(txt))()
File
"/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",
line 452, in OK
self.Apply()
File
"/Applications/Chimera.app/Contents/Resources/share/Movie/VolumeDialog.py",
line 105, in Apply
volumeName=name+" ["+atomType+"]")
File
"/Applications/Chimera.app/Contents/Resources/share/Movie/gui.py", line
356, in computeVolume
self.model.LoadFrame(fn, makeCurrent=False)
File
"/Applications/Chimera.app/Contents/Resources/share/Trajectory/__init__.py",
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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