[Chimera-users] Amber trajectory rmsd

[Eric Pettersen]

Hi George,
	VMD may provide more analysis capabilities in this regard.  The RMSD  
plot you referenced provides a frame-vs.-frame 2D plot of RMSD  
variance for a selected set of atoms.  So if you select the backbone  
atoms (e.g. "sel backbone.full" or Select->Structure->backbone->full)  
and ensure that "Restrict map to current selection, if any" in the  
RMSD dialog is set to true then the resulting plot will be just for  
the backbone atoms.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Jan 5, 2011, at 9:34 AM, George Tzotzos wrote:

> I'd be grateful if you informed if there's a way one can plot  
> protein backbone rmsd fluctuations of trajectories.  I checked
>
> file:///Applications/Chimera.app/Contents/Resources/share/chimera/helpdir/ContributedSoftware/movie/movie.html 
> #rmsd
>
> I may have missed the salient points.
>
> Many thanks in advance
>
> George
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