So far we have considered the behavior of the protein molecules from only the functional perspective, where the configurations of a molecule are defined as biochemically distinguishable species. On the other hand, experiments based on electron microscopy and X-ray diffraction have revealed many structural details about the protein molecules on the thin filament and many hypotheses regarding the structure/function relationship have also been proposed. The correspondence between the state of a finite automaton and the configuration of a protein molecule seems to provide a framework in which the functional and structural information can be combined in a quantitative way by using computer graphics. In this section, we will discuss the graphic representation for the simulation of the muscle thin filament. Before going to the structural details, we first discuss an useful and simple representation of the simulation.