Visualization of chemical concepts can be challenging for many students. This is arguably a critical skill for beginning students of biochemistry to develop, since new information is often presented visually in the form of textbook figures. It is recommended that visual literacy be explicitly taught in the classroom rather than assuming that students will develop this skill on their own. The activity described here is designed to assist students in their development of understanding of basic representations of protein three-dimensional structure as well as various types of ligands (small molecules, ions) through the use of the iPad application PyMOL. It has been used as a laboratory exercise but can also be used in a typical 50-minute class period with a portion of the activity assigned as homework.