Vincent van Mol uses the Modelzilla framework by defining ShapeNode subclasses that each do a different kind of geometrical model of molecular information. It has six such shapes: ribbon and tube shapes for displaying the backbone of proteins or DNA, a balls shape, a molecular surface shape (which uses MSMS to calculate the molecular surface), a ball and stick shape, and a bonds-as-lines shape. The shapes can then be selected for input to operators from other applications that operate on geometries.

There are many options describing how to build each shape. Some options apply across the entire shape, and some apply per molecular element. (A "molecular element" does not refer to the elements of the periodic table, but a piece of a molecule, such as an atom, an amino acid or a bond.) Examples of per-element properties are atom color, atom size, ribbon thickness, width, and color at an amino acid. These properties are kept in a table that has one row per molecular element, and one column per property. The existence of a table row corresponding to a molecular element means the molecular element should be included in the shape. This table was originally a data node extension within Vincent van Mol, which is a good example of fitting complex application data into the framework's data model. The table class was later moved to the framework because of its general utility. The more general framework code has no knowledge of this table type data node. In fact, the only change that was made in moving the table node from Vincent van Mol to the framework was to change the package name at the top of the source file and recompile. This exemplifies the modularity of the system.

Vincent van Mol has special user interface panels for controlling the per-element properties, selecting molecular elements, controlling the creating of shapes, loading molecules, and controlling general settings. Despite the fact that all user input is kept in the repository, it is hard to imagine how the framework could automatically build this user interface. With Vincent van Moll's handmade user interface, the system is as easy to use as any monolithic molecular graphics program. Without the inclusion of the standard framework controls, the user would be unaware that they are using a framework-based system at all. One special user interface panel that controls what molecular elements are included in a rendition is shown in the fogures.

Types of renditions

• Ribbon traces
• Tube traces
• CPK
• Molecular Surfaces (uses MSMS)
• Ball and Stick
• Wire Frame
• Atom and Residue labels