Just released a new version of the Jmol filter for Moodle 3.0 (though should work on recent Moodle 2.x versions) and also adapting to changing browser technologies as they increasingly support HTML5/JavaScript and WebGL and drop support for Java applets.
A significant difference from the previous version is that the filter no longer needs the filter/jmol/temp folder (or the associated filter/jmol/classes and filter/jmol/db folders). This is because most modern browser (Firefox, Chrome, Safari, Opera, Edge) versions can now use JavaScript to directly load binary format chemical structure files from the Moodle file API. This avoids any permissions/security issues with the temp folder and makes the code easier to maintain. After upgrade, you may want to check these folders are removed.
The user can chose, via a drop down menu, between different display technologies; JSmol (HTML5/JavaScript), GLmol (WebGL), or Jmol (Java). JSmol is the default as it has the widest support across recent browsers, supports all the capabilities of Jmol and has reasonable performance on all but the largest chemical stuctures. GLmol is more experimental and does not support all features. However, given WebGL browser/hardware support, does perform well wth larger structures. The 'original' Jmol Java applet has full functionality and performs well. However, support for Java applets has already been dropped (Edge, Chrome), or soon will be dropped (Opera, Safari, Firefox) so this is a 'dwindling' option. That said, Jmol remains an option for those users who prefer, or are institutionally locked-in to, older Java-supporting browsers (e.g. Internet Explorer) and can tolerate Java security pop-ups!
The filter attempts to use a combination of browser-sniffing and feature detection to use the most appropriate display technology - or give an appropriate message if the chosen display technology is not available. The general recommendation is to use the most up-to-date browser you can!
The popup-menu and console buttons have been removed from the bottom panel. You can still get get the popup-menu by right-clicking (or Ctrl-clicking) on the Jmol/JSmol/GLmol instance. This should be familiar to most Jmol users. The console can then be directly selected from the pop-up menu.
The filter is bundled with the latest stable Jmol/JSmol 14.2.x version. The recent Jmol/JSmol 14.4.x release can also be used though I have noticed a few minor issues so not yet included it.
The Jmol filter is available from the Moodle Plugins directory or GitHub.
Please report any issues, requests etc in this forum or on GitHub.