This new function
setKeyboardPassedToPyMOL() in JyMol allows control over whether keyboard events get passed to the underlying PyMol instance (on by default).
JyMol jymol = new JyMol(); jymol.setKeyboardPassedToPyMOL(false); // to turn off
One of the main reasons why this has been added is to be able to control whether users are able to see the text output of PyMol (by pushing escape). This is sometimes useful for development and debugging since it is an easy way to see output from PyMOL.
Note: There is still not a way to type PyMOL commands directly into JyMOL. Since the Cmd infrastructure in PyMOL heavily relies on Python, JyMol still does not have access to it. This is something we will be addressing in future versions of JyMol, so that it can be easier to use and will provide as much functionality as PyMOL.