[Chimera-users] occupancy with pdb trajectory
pett at cgl.ucsf.edu
Tue Dec 4 14:04:59 PST 2007
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?
UCSF Computer Graphics Lab
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
> 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
> mac book pro running Chimera 1.2470.
> BTW I also wasn't able to directly load the gromacs trajectory (tpr
> 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+"]")
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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