Scalable Ambient Occlusion for Molecular Visualisation

Abstract Molecular visualisation tools aid researchers in studying the structure of molecules on desktop computers. Surface features are of importance because these often represent the interface to other molecules. However, local lighting effects, such as Gouraud shading, do not highlight the surface detail of the molecule. We implement a computationally inexpensive approximation of ambient occlusion, a realistic lighting model, which calculates shading based on the occlusion of nearby geometry. Ambient occlusion is expensive to calculate, so we present approximations and optimizations to reduce computation time. This method makes use of the Graphics Processing Unit (GPU) by retrieving the results from depth tests to determine the visibility of surface points. We apply this method to molecular visualisations, focusing on “space-fill” mode where atom sizes represent their atomic radii. We have constructed a stand-alone, prototype test-bed in C++ using OpenGL on the Microsoft Windows XP platform. This prototype is capable of calculating ambient occlusion for molecules in seconds. Various settings can be selected by the user to determine the trade-off between speed of calculations and visual quality of ambient occlusion. High quality ambient occlusion is expensive to calculate, but our method takes as many short-cuts as possible to deliver an acceptable output that is still useful.