Dany Naranjo Feliciano wrote: > Hi: > How could I see with gnuplot my target and template graphics in the same > window, as appear in the tutorial.
You probably don't want to do that in most cases, because the DOPE energy for target and template is not quantitatively comparable. But if you really want to do it, you'll have to correct for gaps. The "plotdope" script in the wiki may be of use to you: http://salilab.org/modeller/wiki/Plotdope
Ben Webb, Modeller Caretaker