Great topic! I agree with the basic premise that the SHAPE results are affected by numerous things besides the presence or absence of the three base pairings that the game's energy model acknowledges. Working to figure out those additional factors is perhaps the most cool aspect of EteRNA.
What tools did you use to create these images? Something other than RNA Composer to predict the 3D structure? And the renderings don't look like options I have seen in Chimera, though there could be plugins I don't know about. I'm especially interested in what you used to predict stacking interactions.
The 3D renderings are no simulations, they are all segments of solved structures from PDB. First, I used FRABASE to identify the PDB entries containing the sequences I was interested in. Then I fetched the structures in Chimera and worked them with it.
Atoms and "normal" bonds are easy to color any way you want, but you need to define your own color to get the the translucid white I applied on the backbone (select/structure/backbone/full). For the hydrogen bonds, I currently like to make them look like springs, but it's an option relatively hard to access: tools/general controls/pseudobond panel/hydrogen bonds/attributes/component pseudobond attribute/bond style
And you're right, there are no built-in command to detect and represent stacking interactions. First, and as I was saying, it took me a very long while (months) before I could find the parameters that validate a stacking interaction. I found them on the website of another 3D rendering tool, PyMol, at http://www.schrodinger.com/kb/1556
Then it's an arduous work in Chimera, but at least it's possible. There are tools in Structure Analysis which allow to define centroids, planes, axis, show or hide these objects, and also to calculate distances and plane angles. Once a pi stacking interaction is validated, I represent the interaction by defining an axis based on the atoms of both aromatic rings.
The other difficulty I had related to this topic was to ascertain whether the izimadole (pentagonal ring in purines) is aromatic or not. I don't recall exactly where I read that they actually are, but considering that reference and the various examples I saw in solved structures, I believe that they are.