This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings indicate that the students possess misconceptions in depicting free atoms, bond angles and ionic and covalent bonds. They limit their models to two dimensional representations and produce models as a series of episodes that follow reaction equations. However, they balance the numbers of atoms and engage with, and discuss, construction of models over extended periods of time. The study concludes that misconceptions may persist from prior learning, may continue due to limited access to prior knowledge, and the individuals may use multiple frameworks to explain new ideas. The "ChemSense" software is discussed as a tool for encouraging discussion and the development of knowledge in chemistry. (Contains 4 figures.)