The JOGL project is the Java Binding for the OpenGL API and has gone through some major changes and enhancements since JyMol 1.0. This project is extremely active and there are a lot of online resources, forums, and documentation on their web site on how to use JoGL. JyMol users and developers will not need to program JoGL directly, but it is useful to know about this project and that JyMol depends on it. JyMol itself uses JoGL for setting up the OpenGL window and its capabilities, but relies on the underlying PyMol implementation that called OpenGL directly.

The most import enhancement that JyMol has gained because of this upgrade to JoGL 2.0 is Support for quad-buffered stereoscopic 3D, which was not available in previous releases.