[Chimera-users] Amber trajectory rmsd

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 5 17:09:48 PST 2011

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 Pettersen
                         UCSF Computer Graphics Lab

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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