This is a basic kit that provides the objects needed to create a nested model(see extras 1,2,3,4). I have provided two different methods (1,2 and 3,4) that were inspired by, "A Soft and Transparent Handleable Protein Model". This kit includes a model to determine clearance, pegs for support and tubes, as well as a cone for creating a funnel.  

The clearance kit provides measures for xy and z clearance in 0.05 intervals. Use the caps with the H to measure z clearance and the caps without the H to measure the xy clearance. Start with the small cap(marked s) at 0.00 and if it goes through all the pegs move to the large cap(marked L). For the xy caps stop at the first one to comfortably fit. For the height caps, stop at the first one to hit the base. The xy measures the difference in radius between the peg and cap. 

For more Information on modeling and printing proteins, visit here. It is still a work in progress, some if the finishing steps can be found here. Feed back is very much appreciated, feel free to leave a comment.