The algorithm for placing struts sounds quite simple. Chimera has ribbon splines that go exactly through the C-alphas, and can also join side chains to a ribbon even when the C-alpha is not on the ribbon. So I think that won't be a problem. The Jmol strut code I looked at looked more complex than what you describe. If it simply chose short distance struts wouldn't you get a bunch of unneeded struts say within one alpha helix, and maybe lack some long range struts that are needed to hold everything together?
Eric Pettersen
UCSF Computer Graphics Lab