This shows the backbone of a protein macromolecule by creating artificial 'backbone' bonds between alpha carbons. Backbone radius can be specified in angstroms.
By default, the backbone bond color is inherited from the atoms (as with other bonds). You can explicitly change the backbone color.

This shows a spline trace of a protein backbone. The hermite spline curve passes through the mid-points between alpha carbon atoms
With color by 'structure' you get different colors for HELIX, TURN, and SHEET. Color by 'amino' and color by 'shapely' assign different colors to different amino acids.

Adapted from http://jmol.sourceforge.net/demo/trace/
gedwards@portjackson.org Sep 2013