Jmol/JSmol MediaWiki Extension
This is an improved version of what runs on Proteopedia, built on top of the original Jmol Extension
Implemented tags: jmol, jmolApplet, uploadedFileContents, wikiPageContents, urlContents, load SMILES, jmolLink jmolMenu jmolCheckbox jmolButton jmolRadioGroup
Not Working Yet tags:
inlineContents (reason: requires inline data)
jmolWikiPopupWindow jmolAppletButton jmolAppletLink jmolFile jmolPdb jmolSmiles (reason: require popup window)
To enable JSmol on your wiki:
Download and expand the latest Jmol (e.g. Jmol-14.0.16-binary.zip ) from http://sourceforge.net
Find and expand jsmol.zip inside the newly created directory
Move the obtained jsmol/ folder into your MediaWiki extensions/ folder

Retrieve a zip archive containing the JSmol Extension files from here
Expanding the zip will create a folder 'wiki' containing all the required files.
Move the wiki/ folder into the folder extensions/jsmol/

Add to your LocalSettings.php file these lines:

require_once( "$IP/extensions/jsmol/wiki/Jmol.php" );
$wgJmolAuthorizeUrl = true;
$wgJmolAuthorizeUploadedFile = true;
$wgJmolAuthorizeJmolPdbTag = true;
$wgJmolAuthorizeChoosingSignedApplet = true;
$wgJmolForceHTML5 = true; // false=uses HTML5 for tablets only , true=always HTML5

To disable this extension simply comment out the require_once line with a numeral (#) sign
Send feedback, suggestions, bug reports to jaime.prilusky@weizmann.ac.il