Ambient occlusion opacity mapping for visualization of internal molecular structure

Abstract

Molecular surfaces often exhibit a complicated interior structure that is not fully visible from exterior viewpoints due to occlusion. In many cases this interior cavity is the most important feature of the surface. Applying standard blended transparency can reveal some of the hidden structure, but often results in confusion due to impaired surface-shape perception. We present ambient occlusion opacity mapping (AOOM), a novel visualization technique developed to improve understanding of the interior of molecular structures. Ambient occlusion is a shading method used in computer graphics that approximates complex shadows from an ambient light source by rendering objects darker when surrounded by other objects. Although ambient occlusion has previously been applied in molecular visualization to better understand surface shape, we instead use ambient occlusion information to determine a variable opacity at each point on the molecular surface. In this manner, AOOM enables rendering interior structures more opaque than outer structures, displaying the inner surface of interest more effectively than with constant-opacity blending. Furthermore, AOOM works for cases not handled by previous cavity-extraction techniques. This work has been driven by collaborators studying enzyme-ligand interactions, in which the active site of the enzyme is typically formed as a cavity in the molecular surface. In this paper we describe the AOOM technique and extensions, using visualization of the active site of enzymes as the driving problem.