Wikipedia:Using Jmol to display molecular models
"Using Jmol to display molecular models" is work in progress to use the Jmol applet to display molecular models of chemical and biochemical molecules in Wikipedia articles. Jmol is now frequently used in standard HTML pages to display molecules which can then be manipulated using the mouse. NicoV has put up a reference page for the now fully functional Jmol Mediawiki extension on the Jmol wiki. Please, post suggestions for further development on the Jmol extension in the discussion page of the Jmol extension on the new Jmol Wiki which, like Wikipedia uses MediaWiki.
To display molecules with Jmol, your browser needs to be Java enabled. Two examples of Jmol images in a wiki are here and here. These use Jmol to show medium sized molecules with buttons to control the rotation of the molecules. The right mouse button opens a Jmol menu while the left mouse button can be used to move the image.
The use of Jmol in HTML pages involves downloading a data file containing the atomic types and cartesian coordinates. Most simply, the molecular data can be in the page itself between tags. The molecular data can also be in a wiki page, such as a subpage of the article displaying the molecule, or by uploading the molecular data file to the wiki or perhaps on Wikipedia to Commons like the use of images. Chemists have developed many different formats for files of molecular coordinate data and most of these are readable by Jmol.
Use of Jmol in Wiki pages is available for several wikis (see Jmol-Wiki extensions), and contributions have been made by several people. NicoV has completed work on the second version of the Jmol extension adding support for Jmol in MediaWiki. This uses two PHP files rather than the one used in the initial implementation. This was implemented for mediawiki 1.12, but a bug that prevented it working with later versions was fixed in late November 2008. It is proposed to get this fully working on Wikipedia and Wikiversity in a way that editors can easily add Jmol molecules to articles on chemistry and biochemistry.
The delay in implementing Jmol in mediawiki has been that security concerns have been raised. There is indeed a security concern as illustrated here (has been fixed). There is a related issue of support for the Chemical Markup Language (CML) and a bug report has been submitted here for both Jmol and CML. We need technically minded editors to address these issues.
If you are interested in helping please add your name below using ~~~~, keep a watch on this page and on Wikipedia talk:WikiProject Chemistry, and add your suggestions to Wikipedia talk:Using Jmol to display molecular models.
Update 4/2011: [http://chemapps.stolaf.edu/jmol/jmol.php] now allows creation of external links to any model from any server and direct SMILES-to-3D conversion displayed in an applet in a new window or tab. Model files need not be present; all that is needed is a SMILES string or chemical identifier such as a chemical name or InChI key. For example: [aspirin from name]. See Wikipedia_talk:WikiProject_Chemicals#IRC_meeting_to_discuss_possible_addition_of_Jmol_links for several more examples. Hansonrstolaf (talk) 11:44, 8 April 2011 (UTC)