Automatically identifying protein conformations can yield multiple candidate structures. Potential candidates are examined further to cull false positives. Individual conformations and the collection are compared when seeking flaws. Desktop displays are ineffective due to limited size and resolution. Thus a user must sacrifice large scale content by viewing the micro level with high detail or view the macro level while forfeiting small details. We address this ultimatum by utilizing multiple, high resolution displays. Using 27, 50", high resolution displays with active, stereoscopic 3D, and modified virtual environment software, each display presents a protein users can manipulate. Such an environment enables users to gain extensive insight both at the micro and macro levels when performing structural comparisons among the candidate structures. Integrating stereoscopic 3D improves the user’s ability to judge conformations spatial relationships. In order to facilitate intuitive interaction, gesture recognition as well as body tracking are used. The user is able to look at the protein of interest, select a modality via gesture, and the user’s motions provide intuitive navigation functions such as panning, rotating, and zooming. Using this approach, users are able to perform protein structure comparison through intuitive controls without sacrificing important visual details at any scale.