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Bioinformatics Vol. 19 no. 8 2003
Pages 913-922
© 2003 Oxford University Press

FPV: fast protein visualization using Java 3DTM

Tolga Can *, Yujun Wang , Yuan-Fang Wang and Jianwen Su

Department of Computer Science, University of California at Santa Barbara, Santa Barbara, CA 93117-5110, USA

Received on June 9, 2002 ; revised on September 11, 2002 ; accepted on September 11, 2002

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 organizing 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 effectiveness of the proposed method by comparing the visualization 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 improvement in rendering speed and could load molecules three times as large as the previous systems could.

Availability: FPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/

Contact: tcan{at}cs.ucsb.edu

* To whom correspondence should be addressed.


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