This study presents a RasMol-based assessment instrument for the evaluation of the outcomes of protein structure learning. The instrument formulated by this study consists of a RasMol-based project, a set of assessment criteria, and a post-project task for students at the introductory level of biochemistry. The samples involved in the experimental teaching were the students enrolled in the biochemistry course in National Pingtung Teachers College. This study found that, in general, students who meet the criteria usually display sufficient knowledge of protein structure upon the completion of their project. From the students' feedback, it was also evident that this project is a constructive and effective way to learn about the essentials of the protein structure. Therefore, visualization software such as RasMol can be used as a teaching tool as well as an assessment instrument.