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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