[Chimera-users] occupancy with pdb trajectory

[Eric Pettersen]

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__'
>
>
> -- 
>
> Andrea C. Vaiana
> Theoretical Biology and Biophysics
> Mail stop K710, T-10
> Los Alamos, NM 87545
> Los Alamos National Laboratory
>
>
>
>
>
>
>
>
>
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