3D models derived from actual molecular structures have the potential to transform student learning in biology. We share findings related to our research questions: 1) what types of interactions with a protein folding kit promote specific learning objectives?, and 2) what features of the instructional environment (e.g., peer interactions, teacher involvement) affect learning? We provide a framework for categorizing ways of using the models that can be used as evidence for whether and how physical models promote molecular understanding. [This paper was published in "Learning and becoming in practice: The International Conference of the Learning Sciences (ICLS)," 2014, Volume 1 (pp 1583-1585. Boulder, CO: International Society of the Learning Sciences. ]