JyMOL v1.1

JyMOL infrastructure has been modernized to allow us to more quickly port functions from PyMOL into JyMOL.

bgRgb - Sets background color
button - Sets a button's function
setButtonMode - Sets the button mode. This allows for all mouse modes, including Editing and the emulation of Maestro.
mplay - stops/plays/toggles the movie
feedback - changes the amount of information output by pymol
rock - changes rock mode
mapNew - creates or updates a map object
turn - rotates the camera about one of the three primary axes, centered at the origin
get - gets one of JyMOL's built-in settings
getObjectNames - gets names of all or enabled objects
getRepsForObject - gets all representations that have been turned on specifically for a particular object
getRepsInSceneForObject - gets all representations for a particular object that have been turned on in a scene

Support for quad-buffered stereoscopic 3D
added invokeLater() for JyMol to avoid collisions between JyMOL interactions and heavy computations (e.g., with AWT).
added setKeyboardPassedToPyMOL() for JyMol to control whether debug log is shown from within JyMOL by pressing Escape (On by default)
support reading MacroModel files
enhanced and generalized the JyMOLApplet class with functions that make it easy to call commands dynamically, and from scripts, within an Applet. (source code is available as well in the src directory)

JOGL version 2.0
Conversion of proprietary JAVA->C interface to SWIG
- makes it easier to add functionality to JyMOL
added GLEW to allow JyMOL to be able to configure/use GLSL shaders
Transitioning from JyMOL 1.0/Changes to JAVA dependent code
- moved com.delsci.jymol to com.schrodinger.jymol
- Simplified some commands so that they no longer need to pass the array lengths manually (e.g., rampNew(), setView(), selectList())
- Functions that changed names
- JAR file names have changed, classpath needs to be updated
Fixed Miscellaneous Bugs

PyMOL Documentation