FPV: Fast Protein Visualization Using Java 3D

You can download FPV (with source code) at the following link:
FPV.zip

Updated FPV.zip on 10:10PM (GMT-8) November 05 2004:
- Added new coloring schemes (by CPK, by secondary structure, and by chain). The coloring schemes can be applied to all models except the ribbon model, which always uses the "Color by Secondary Structure" scheme.
- Added "Change Sphere Quality" (i.e., number of sphere subdivisions) to the menu.
Updated FPV.zip on 04:10PM (GMT-8) June 26 2004:
- Changed Mouse/Keyboard controls.
- Added "Start/Stop Animation" to the menu.
Updated FPV.zip on 09:10PM (GMT-8) May 22 2003:
- Changes: File path info for PDB Data is changed to follow Unix style,
  i.e. "/", so that it now runs under Unix, Linux, and Windows.
Updated FPV.zip on 11:25AM (GMT-8) May 23 2003:
- Changes: Another Windows style path in biopackage/graphics/SceneBuilder.java
  is changed to follow Unix style.
Updated FPV.zip on 10:03PM (GMT-8) May 26 2003:
- Corrected a bug related to centering the 3D structure.
- Added a menu bar for opening new molecules, changing model types,
  and showing sequence and tree views.

Java 3D API : DOWNLOAD
Make sure you have Java3D properly installed and you can run the HelloUniverse demo that comes with the Java3D installation.

Unzip FPV.zip
Using command prompt go to the directory where you unzipped FPV.zip.
Type FPV <pdb id>, e.g. FPV 1a0s, from the command prompt. If "pdb id" is one of the file names under "data" directory the PDB file will be loaded locally, otherwise it will be fetched from PDB web site using internet connection.

T. Can, Y. Wang, Y.-F. Wang and J. Su, "FPV: fast protein visualization using Java 3D", Bioinformatics, 19(8):913-922, 2003. Link
T. Can, Y. Wang, Y.-F. Wang and J. Su, "FPV: Fast Protein Visualization Using Java 3D", in Proceedings of the 18th Annual ACM Symposium on Applied Computing, SAC'03, pp. 88-95, Melbourne, FL, March, 2003. PDF
ACM SAC'03 Presentation Slides : tcanSAC03.pdf

FPV is tested on a Windows environment. It should run without a problem on any environment where Java and Java3D are installed.
You can contact if you have any problems running FPV.