Modeling is a practice of science that is underemphasized in biology classrooms in comparison to its central focus in the physical sciences. Visualizations of the submicroscopic world of molecules are becoming increasingly sophisticated with the evolution of new technologies. With this in mind, we introduced high school biology classrooms to a professional molecular modeling software program used by research biochemists to visualize proteins and other macromolecules. Analysis of surveys completed before and after the use of the program revealed significant student gains in their understandings of the nature of models. Student and teacher perceptions of the program showed an appreciation for the real/authentic nature of the program, and its affordances when utilizing the three-dimensional rendering of proteins. The teachers did report a general level of frustration regarding their lack of experience with the program and their inability to unlock its full potential due to not being able to access all of the program's features. However, we believe that the evidence at hand indicates that the value of introducing students to authentic molecular modeling tools in high school science classrooms outweighs the potential limitations..