FPV: fast protein visualization using Java 3DTM

Motivation: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3DTM are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D 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. Results: In this paper we present techniques for organiz-ing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effec-tiveness of the proposed method by comparing the visu-alization component of our system with two other Java 3D 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 im-provement in rendering speed and could load molecules three times as large as the previous systems could. Availability: FPV is freely available with source code a