Heretic, I think you need to have a new "vision" for how the sodaconstructor works. The structure of a sodaconstructor model is just a bunch masses connected by spring of whatever length you choose - the applet doesn't care what order they were made in, or how they look in construct mode; the structure is "set". You simply connect the masses the way you wish to, using guidelines to measure this. Once you understand this fully, you will see how much control you have, and you won't wonder things like "how do I connect this."
If this suggestion was completely off-base, I apologize.
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