Wikipedia:Using Jmol to display molecular models: Difference between revisions

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Work"'''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. However, the use within Wiki pages still needs some more work. [[m:User:NicoV|NicoV]] has put up a [[m:User:NicoV/Jmol Extension|MediaWiki article]] andon moremeta. detailThere inis a [http://fahwikiwiki.netjmol.org/index.php?title=Jmol_MediaWiki_Extension/MediaWiki Folding@Homereference articlepage]. Thefor latterthe usesnow Jmolfully tofunctional showJmol aMediawiki mediumextension. sizedPlease, moleculepost withsuggestions buttonsfor tofurther controldevelopment on the rotationJmol ofextension in the molecule[http://wiki.jmol.org/index.php/Talk:MediaWiki neardiscussion the bottompage] of the page.Jmol Yourextension browseron needsthe to benew [[Java]] enabledhttp://wiki.jmol.org/ ThisJmol pageWiki] shouldwhich, belike consultedWikipedia asuses an example of what is possibleMediaWiki.
 
To display molecules with Jmol, your browser needs to be [[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 new [http://wiki.jmol.org/ Jmol Wiki] using MediaWiki is now online. The '''reference page for the Jmol extension''' can be found [http://wiki.jmol.org/index.php/MediaWiki there]. This extension is fully functional. 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.
 
The use of Jmol in HTML pages involves downloading a data file containing the atomic types and cartesian coordinates. ThisMost cansimply, bethe alsomolecular donedata can be in the wiki,page eitheritself bybetween puttingtags. theThe 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. MoreChemists simply,have thedeveloped many different formats for files of molecular coordinate data canand bemost inof thethese pageare itselfreadable betweenby tagsJmol.
 
Use of Jmol in Wiki pages is available for several wikis (see [http://wiki.jmol.org/index.php/Jmol_Processor Jmol-Wiki extensions]), and contributions have been made by several people. [[m:User:NicoV|NicoV]] has completed work on the first version of the Jmol extension adding support for Jmol in MediaWiki. It is proposed to get this fully working on Wikipedia in a way that editors can easily add Jmol molecules to articles on chemistry and biochemistry.