FPV: Fast Protein Visualization Using Java 3DTM

We have developed a protein visualization system based on Java 3DTM. Java 3D provides compatibility among different systems and enables applications to be run remotely through web browsers. However, using Java 3DTM for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3DTM are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We demonstrate the effectiveness of these techniques by comparing the visualization component of our system with two other Java 3DTM based molecular visualization tools. In particular, for Van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could.