Wikipedia:Using Jmol to display molecular models: Difference between revisions
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"'''Using Jmol to display molecular models'''" is work in progress to use the '''[[Jmol]] applet''' to display [[molecule|molecular]] models of [[chemistry|chemical]] and [[biochemistry|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. [[m:User:NicoV|NicoV]] has put up a [[m:User:NicoV/Jmol Extension|MediaWiki article]] on meta. There is a [http://wiki.jmol.org/index.php/MediaWiki reference page] for the now fully functional Jmol Mediawiki extension. Please, post suggestions for further development on the Jmol extension in the [http://wiki.jmol.org/index.php/Talk:MediaWiki discussion page] of the Jmol extension on the new [http://wiki.jmol.org/ Jmol Wiki] which, like Wikipedia uses MediaWiki.
To display molecules with Jmol, your browser needs to be [[Java (programming language)|Java]] enabled. Two examples of Jmol images in a wiki are [http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension here] and [http://wiki.jmol.org/index.php/User:Bduke 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.
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