Computer-based learning tools include design features to enhance learning but learners may not always perceive the existence of these features and use them in desirable ways. There might be a gap between what the tool features are designed to offer (intended affordance) and what they are actually used (actual affordance). This study thus aims at investigating how the design features of a computer-based tool supported high school students' modeling practices in atmospheric sciences. Twenty-three 10th graders participated in 16 hours of learning activities by using the tool. We conducted a detailed analysis of students' computer activities, their use of the design features, and their building, testing, analyzing, and evaluating practices. The analysis showed that while some design features such as "Variable List" and "Testing Variables" were perceived by students and successfully afforded their enactment of building and analyzing practices, other features including "Screen Shot" and "Edit" were rarely used or not utilized in the desirable ways. Based on the findings, this study suggests that the realization of intended affordances may involve factors of learners' characteristics, the nature of learning activities, and the complexity of tasks, and constructs an affordance analysis scheme to inform the design of computer-based learning tools.