carma -v -rms -mrms 2.0 fitted.dcd native.psf
The mrms flag tells carma to draw (in the rmsd plot) as black everything with an rms deviation larger that 2.0 Angstroem. The resulting postscript images (fitted.dcd.averag.ps and fitted.dcd.rmsdev.ps) can be view with, say, gv.
You can aid your analysis with
carma fitted.dcd.rmsdev.ps fitted.dcd.averag.ps