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

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Line 5: 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 [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~~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. <s>There is indeed a security concern as illustrated [http://wiki.jmol.org/index.php/User:Ilmari_Karonen/JS_injection_demo here]</s> (has been fixed). There is a related issue of support for the [[Chemical Markup Language]] (CML) and a bug report has been submitted [https://bugzilla.wikimedia.org/show_bug.cgi?id=16491 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 <nowiki>~~~~</nowiki>, 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 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: [[http://chemapps.stolaf.edu/jmol/jmol.php?model=aspirin&width=500&caption=aspirin%20model aspirin from name]]. See [[Wikipedia_talk:WikiProject_Chemicals#IRC_meeting_to_discuss_possible_addition_of_Jmol_links]] for several more examples. [[User:Hansonrstolaf\|Hansonrstolaf]] ([[User talk:Hansonrstolaf\|talk]]) 11:44, 8 April 2011 (UTC) ==Helpers== Line 13 ⟶ 17: * [[User:Benjah-bmm27\|Ben Mills]] 10:52, 9 March 2006 (UTC) * [[m:User:NicoV\|NicoV]] 18:34, 8 April 2006 (UTC) * [[User:AngelHerraez\|AngelHerraez]] ([[User talk:AngelHerraez\|talk]]) 17:21, 7 June 2009 (UTC) ==See also== [[Wikipedia_talk:WikiProject_Chemicals/Archive_2011#IRC_meeting_to_discuss_possible_addition_of_Jmol_links]] ==External links== Line 18 ⟶ 26: [http://wiki.jmol.org/ Jmol Wiki] [http://wiki.jmol.org/index.php/Jmol_Processor Jmol-Wiki extensions] *[http://wiki.jmol.org/index.php/MediaWiki Jmol Mediawiki extension] [[Category:WikiProject Chemistry\|Jmol]]