Molecular CAD tools are required to design diamondoid nanostructures in full atomic-detail.
Crystal Sketchpad (formerly Crystal Clear) is a molecular CAD tool which allows the design of simple diamondoid structures. Here is a paper describing the design of a conveyor belt using Crystal Sketchpad presented at the Fourth Foresight Conference on Nanotechnology. Or the postscript if you prefer.
The most complicated structure I have designed with CrystalSketchpad is the conveyor system below ...
Large version (80k)
and there is also a VRML model of it.
An SGI executable of Crystal Sketchpad is available (mips2 instruction set). To run the program type "cs < data".
Crystal Sketchpad began as
A paper about Crystal Clear which appeared in the journal Nanotechnology. You also need the postscript for the main figure.
Some structures designed using Crystal Clear are available as pdb files.
Pictures of various structures follow.