Hi Andrea, I _believe_ this indicates that your frames aren't consecutively numbered. Is your PDB input a single file with multiple MODEL records. If so, are the numbers on these MODEL records consecutive? Chimera should probably handle non-consecutive numbering (at least when there's a regular "stride") but it doesn't yet. I'd also be interested in looking at your tpr/trr problem if you could get the files to me. How big are they? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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__'
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Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory
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