Classroom response systems are an important tool in many active learning pedagogies. They support real-time feedback on student learning and promote student engagement, even in large classrooms, by allowing instructors to solicit an answer to a question from all students and show the results. Existing classroom response systems are general purpose and not tailored to the specific needs of a chemistry classroom. In particular, it is not easy to deploy molecular representations except as static images. Here we present the 3Dmol.js learning environment, a classroom response system that uses the open-source web-based 3Dmol.js JavaScript framework to provide interactive viewing and querying of 3D molecules. 3Dmol.js is available under a BSD 3-clause open-source license, and the learning-environment features are all available through http://3dmol.csb.pitt.edu/ without any software installation required.