Illustrations of molecular models are widely used for the study and dissemination of molecular structure and function. Several metaphors are commonly used to create these illustrations, and each captures a relevant aspect of the molecule and omits other aspects. Effective tools are available for rendering atomic structures by using several standard representations, and the research community is highly sophisticated in their use. Molecular properties, such as electrostatics, and large complex molecular and cellular systems currently pose challenges for representation.

MGLtools is a collection of methods for visualization and analysis of biomolecular systems, including ADT (the graphical front end of AutoDock), PMV (a customizable molecular viewer) and Vision (a visual programming environment for visualization).

ePMV (embedded Python Molecular Viewer) runs molecular modeling software embedded within professional 3D animation applications, such as Maya and Cinema4D.

Tangible Interfaces for Molecular Interaction combine 3D physical models of molecules with augmented reality.