Ice Crystal Matrix measurements of H2O molecules?
You can produce STL (and VRML) files directly from Mercury - see https://www.ccdc.cam.ac.uk/Community/blog/post-56/

I'm not sure how best you'd go about including female sockets for bike spoke segments, but be aware that for some 3D printing types you're charged for the total volume of material used, so you might be better off trying to create a model with multiple molecules in a smaller area with less empty space.