On Aug 16, 2013, at 5:46 PM, Tom Goddard <goddard@sonic.net> wrote:
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?
If you use pseudobonds rather than cylinders with hard-coded coordinate endpoints, it won't matter whether the ribbons go through the C-alpha positions or not. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu