====== jmol2 Plugin ======

---- plugin ----
description: Plugin for Jmol applet that displays 3D-molecular models
author     : Luigi Micco
email      : l.micco@tiscali.it
type       : syntax
lastupdate : 2010-02-17
compatible : Lemming
depends    : 
conflicts  : 
similar    : 
tags       : !obsolete, biology, chemistry, science

downloadurl: https://trello.com/1/cards/5b0471fc76ee75277635d4df/attachments/5b047227cf5c5f118ca3eefd/download/jmol2.zip
bugtracker : 
sourcerepo : 
donationurl: https://www.paypal.com/cgi-bin/webscr?cmd=_s-xclick&hosted_button_id=KHHGCTLSQPGEJ

screenshot_img: 
----

Java applets such as used in this plugin are not supported in recent browsers anymore. Jmol seems to have html5 based variant, but not implemented here.

===== Download and Installation =====

Search and install the plugin using the [[plugin:extension|Extension Manager]]. Refer to [[:Plugins]] on how to install plugins manually. If you do install manually the directory must be named ''jmol2''.

To see a demo online, visit [[http://www.pkuinfo.it/pku/risorse/modello_molecole|pkuinfo.it]].

===== Overview ====

The goal of this plugin was to provide a simple, ready to go system viewer for chemical structures in 3D. It also bundles the necessary java libraries (**hence the 6.5Mb size**) so that you should not need to do any configuration to get it up and running as quickly as possible. I haven't thoroughly tested this point on many platforms yet, so any feedback is welcome.

===== Features =====

  * Uses the [[http://jmol.sourceforge.net/|Jmol]] JavaScript library, an open-source Java viewer for chemical structures in 3D.

===== Issues and Requests =====

This package uses a library maintained by someone else which is just focusing on use Jmol into DokuWiki content. 

===== Sites using this plugin =====

  * [[http://www.pkuinfo.it|PKUinfo: Informazioni, domande e risposte sulla fenilchetonuria]] 

===== Version history =====

  * **''2010-02-17''** (current)\\ first release

=====  How to use =====

Use 'jmol' tag and put the filename of a 3D-molecular models file inside of it. You can set the size of applet and the background color, after the filename.

<code>
<jmol ({{namespace:molecule}}) (width) (height) (background)>
  ... Jmol scripts ...
</jmol>

....

<jmol>
  ... more Jmol scripts ...
</jmol>
</code>

===== Examples =====

  * See [[http://www.pkuinfo.it/pku/risorse/modello_molecole|some 3D models]]

===== Discussion =====

There's always room for improvement. If you're able to add any contributions to make jmol2 better, please [[l.micco@tiscali.it|let me know]] or discuss your thoughts right here (please use ''<nowiki>===== Level 3 Headlines =====</nowiki>'' to open a new "thread"/issue and ''<nowiki>----</nowiki>'' (four dashes, horizontal rule) to structure it when needed).