Jmol Processor

Running Jmol / JSmol

• Jmol as a standalone application.
• J(S)mol as a web applet or HTML5 object.
  • compatibility with JavaScript frameworks or libraries.
• J(S)mol embedded in wikis or blogs.
• Borrowed JSmol, or running JSmol without your own server.
• Running Jmol using Java Web Start.
• JSmol in a Jupyter notebook.
• Jmol in an Android tablet.
• Troubleshooting.

Jmol in Wiki's

The Jmol Applet can be embedded in Wiki pages, like in HTML pages. Below are four processors for four different Wiki engines (MediaWiki, MoinMoin, MoniWiki and UniWakka).

Jmol in DokuWiki

A DokuWiki plugin allows to display Jmol applets with files from the 'pdb' namespace.

Once the wiki is properly configured, the code for inserting Jmol looks like this:

<jmol (filename) (width) (height) (button)>
  ... Jmol scripts ...
</jmol>

It is possible to put a button so the model is loaded later, as well as to use Jmol.js functions.

Jmol in MediaWiki

A fully functional JmolProcessor has been written for MediaWiki. Check the MediaWiki page. It has been installed on this Wiki.

Jmol in MoinMoin

Now we have a small JmolProcessor for MoinMoin, which works similar the JmolProcessor for MoniWiki.

1. open a source-code section with three curly braces ({{{) followed by #!Jmol (note the capital J).
2. this and all following lines beginning with a "#" character may include the following options:

height="pixel", width="pixel", frank="on|off", script="JmolScript"

other options are not supported

1. insert the source-code of the molecule
2. close the section with three curly braces (}}})

Example:

{ { {#!Jmol frank='on'
# height="150" width="150"  
# script='cpk 0.3; wireframe 0.1'
ATOM      1  O   UNK     1       0.000   0.000   0.000  1.00  0.00
ATOM      2  H   UNK     1       0.943   0.000   0.000  1.00  0.00
ATOM      3  H   UNK     1      -0.259   0.907   0.000  1.00  0.00
ATOM      4  O   UNK     1       3.000   0.000   0.000  1.00  0.00
ATOM      5  H   UNK     1       3.568   0.000   0.753  1.00  0.00
ATOM      6  H   UNK     1       3.568   0.000  -0.753  1.00  0.00
END
} } }

A separate mechanism for MoinMoin is described in MoinMoin Macros.

Jmol in MoniWiki

A processor has been written for MoniWiki (MoniWiki is a PHP clone of the MoinMoin) to embed the JmolPlugin. It use the Processor feature of MoinMoin.

A demo is online: http://chemie.skku.ac.kr/wiki/wiki.php/JmolPlugin

Note that the Jmol Applet is slightly modified to enable Clipboard feature. You can grab a image with a 'Y' key on the applet : type 'y' on the applet and type 'D' to toggle the rendering method. --WkPark

The code that can be embedded in Wiki pages in MoniWiki looks like:

#!jmol (-)
ATOM      1  O   UNK     1       0.000   0.000   0.000  1.00  0.00
ATOM      2  H   UNK     1       0.943   0.000   0.000  1.00  0.00
ATOM      3  H   UNK     1      -0.259   0.907   0.000  1.00  0.00
ATOM      4  O   UNK     1       3.000   0.000   0.000  1.00  0.00
ATOM      5  H   UNK     1       3.568   0.000   0.753  1.00  0.00
ATOM      6  H   UNK     1       3.568   0.000  -0.753  1.00  0.00
END

Jmol in UniWakka

A processor has been written for UniWakka, a PHP-powered wiki, to embed the Jmol applet. It uses a customised actions/ feature of UniWakka and accesses data files (.mol, .pdb, whatever) stored within the UniWakka database. The demo is known to work on Mac OSX (Safari, FireFox, Camino, Explorer) and Windoze (Explorer, Opera, FireFox)

A demo is online: http://www.shef.ac.uk/chemistry/uniwakka/

See also Help On Parsers.

Contributors

NicolasVervelle, AngelHerraez, Pimpim, TylerOderkirk