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...Used in conjunction with the Jmol JavaScript Object (http://wiki.jmol.org/index.php/Jmol_Javascript_Object), JSmol seamlessly offers alternatives to Java on these non-Applet platforms.
JSmol can read all the files that Jmol reads. You can do all the scripting that Jmol does. You can create all the buttons and links and such that you are used to creating for Jmol. All of the rendering capability of the Jmol applet is there. JSmol has both a console and a popup menu.
JSmol is integrated fully with JSME and JSpecView.
A "lite" version of JSmol provides minimal functionality (balls and sticks only) for extremely small-bandwith apps.
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...Complete editing of PDF documents is possible with PDFedit. You can change raw pdf objects (for advanced users) or use many gui functions. Functionality can be easily extended using a scripting language (ECMAScript).
Emma (Extensible Multi Media Architecture) is an open-source, modular, extensible, dynamic framework for declarative authoring and display of 2D and 3D interactive multimedia. It uses Lua for scripting and Ogre3D for rendering. http://www.emma3d.org