Interactive Analysis of Connolly Surfaces for Various Probes

Abstract

The Connolly surface defines the boundary between a molecular structure and its environment. Its shape depends on the radius of the probe used to inspect the structure. The exploration of surface features is of great interest among chemists because it helps them to better understand and describe processes in the molecular structure. To help chemists better explore these features, we have combined two things together: a fast extraction of Connolly surfaces from a Voronoi diagram of atoms and a fast visualization based on GPU ray casting. Not only the surface but also the volume description is provided by the diagram. This enables to distinguish surface cavities one from another and compute their properties, e.g. the approximate volume, the maximal filling sphere or the maximal probe that can escape from the cavity to the outer environment. Cavities can be filtered out by applying restrictions to these properties. Views behind the surface and surface clipping improve the perception of the complex internal structure. The surface is quickly recomputed for any probe radius, so interactive changes of the probe radius show the development of cavities, especially how and where they merge together or with the outer environment.The Connolly surface defines the boundary between a molecular structure and its environment. Its shape depends on the radius of the probe used to inspect the structure. The exploration of surface features is of great interest among chemists because it helps them to better understand and describe processes in the molecular structure. To help chemists better explore these features, we have combined two things together: a fast extraction of Connolly surfaces from a Voronoi diagram of atoms and a fast visualization based on GPU ray casting. Not only the surface but also the volume description is provided by the diagram.