WM3D is a flash11 molecular viewer for various kinds of molecules. This viewer is based on Watermelon and a sample program written by Nicolas Cannasse. Molecules can be shown in spheres, sticks, tubes, and ribbons.
Here are some sample screenshots of WM3D. (i couldn't embed flash11 swf files to this wiki. see sample swfs in src/samples.)
(2012/03/17)Sample movie is available on the project webpage.
(2012/06/16)ATPase sample movie is available here. Flash player 11.2 or later will be required. (Flash player 11.1 complains but can play movie.)
(2012/12/17-18)C60 molecular orbital (MO) sample is available here. Currently, only flat shading is available for drawing MO. The python script which generate xml data from gamess log file will be included in the next release.
WM3D 0.4x is licensed under MPL2.0. Python scripts in WM3D 0.4x is licensed under MIT License. WM3D 0.3x is licensed under MPL1.1/GPL2.0+/LGPL2.1+ trilicense.
WM3D is tested only on Linux (Debian/testing(wheezy) Fedora15) and Windows XP. It may be possible to use in other platforms, though not tested.
See wiki:wm3d/Setup for details.
See wiki:wm3d/HowToUse for details.
WM3D is, honestly speaking, not a user-friendly program, especially for Windows users. A plugin for VMD is available, which works both on Windows and Linux.
See wiki:wm3d/VMD_Plugin for detail.
edit