- Jmol as a standalone application.
- J(S)mol as a web applet or HTML5 object.
- 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.
Jmol (JSmol) Extension for MediaWiki, version 5
For general information on this Extension and particularly about how to install and set it up, visit the MediaWiki page.
This version of the Extension has been developed and tested with MediaWiki 1.32.
It will use by default JSmol objects in the HTML5 modality, but configuration may be adjusted to allow the Java modality (signed applet) or the WebGL modality (note that JSmol has limited functionality with the latter). All mentions of either Jmol or JSmol in this documentation are synonyms. Note also that the use of "applet" in names and references is maintained for legacy reasons but Java is not involved any more (unless forced by the user and allowed by the wiki administrator).
- Please check the version you have installed in your wiki (browse to Special pages, then Version). Documentation for former versions of the Extension may be found in MediaWiki/ExtensionV3 and MediaWiki/ExtensionV4.
How to use the Jmol Extension
This applies to version 5 of the Extension
There are 4 tags that will render a link in the page that, when clicked by the user, will open a small window (pop-up) with a JSmol panel that displays a structure. No custom rendering or scripting on the structure is possible.
See MediaWiki/Simple_Tags for details and demonstration with examples.
jmol tag encloses different subtags that offer more flexibility in how and when the model will be displayed,
as well as its rendering or scripting.
jmolAppletLinkboth will, upon user action, open a small window (pop-up) with a JSmol panel displaying the structure. See MediaWiki/Tags for Pop-up Models for details.
jmolAppletInlineLinkboth will, upon user action, insert into the page a JSmol panel displaying a structure. See MediaWiki/Tags for Pop-in Models for details.
jmolAppletinserts the JSmol panel in the page as soon as it is loaded. See MediaWiki/Tags for In-page Models for details.
jmolButtonThis and the following insert in the page controls to act on one
jmolApplet. See MediaWiki/Tags for Controls for details.
jmolApplet, same as all the above ones
scriptWhenCheckedapplies only to
scriptWhenUncheckedapplies only to
checkedapplies only to
itemapplies only to
verticalapplies only to
menuheightapplies only to
For documentation on former versions of the Extension, see MediaWiki/ExtensionV3 and MediaWiki/ExtensionV4.
- A few basic examples of the <jmolFile>, <jmolPdb> and <jmolSmiles> tags.
- A demo page for the <jmol> tag
- Uploaded XYZ File -- includes test of <jmolCheckbox>, <jmolLink>, <jmolButton>, and <jmolMenu>
- Uploaded MDL Molfile
- Uploaded CML File
- Uploaded PDB File opening in a pop-up -- tests
- Inlined MDL Molfile
- Inlined PDB File
- Inlined CML File
- Load SMILES via script -- Includes test of signed applet and <jmolMenu>
- Test page (Brian's)