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As much as I would like to recommend Sage for this project, I have a feeling that this is not the optimal solution for what you want to do. I wouldn't be surprised if one could use Jmol directly for doing this? While it would be possible to do this in Sage (you could look at the documentation for spheres or for implicit plots for cylinders, and then use the @interact functionality for moving things), it would be quite elaborate to do; Sage is a mathematics program with graphics capability, not a graphics program with math capability. Ideally there is probably a drag-and-drop program that already does this, in fact.