Increasingly, multi-representational educational technologies are being deployed in science classrooms to support science learning and the development of representational competence. Several studies have indicated that students experience significant challenges working with these multi-representational displays and prefer to use only one representation while problem solving. Here, we examine the use of one such display, a multi-representational molecular mechanics animation, by organic chemistry undergraduates in a problem-solving interview. Using both protocol analysis and eye fixation data, our analysis indicates that students rely mainly on two visual-spatial representations in the display and do not make use of two accompanying mathematical representations. Moreover, we explore how eye fixation data complement verbal protocols by providing information about how students allocate their attention to different locations of a multi-representational display with and without concurrent verbal utterances. Our analysis indicates that verbal protocols and eye movement data are highly correlated, suggesting that eye fixations and verbalizations reflect similar cognitive processes in such studies. (Contains 5 tables, 4 footnotes and 4 figures.)