The question: "Is there a way to put sketch objects into plot files? I have a beautiful picture on the screen (created using sketch commands) but don't seem to be able to get it out through plot_on/plot_off. No matter what I do, the plot file contains only the line drawing of the mol_objects."
Morten explained: "You should be able to do it. Sometimes, the polygons are in the plot file, but are not instanced and therefore not displayed on the plot. Try defining the object explicitly, using sketch_object, *after* you have chosen plot_on.
If you are plotting CPK spheres, be sure to choose mode solid for the spheres in Sketch_setup."