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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users