CMS Using Jmol

From Jmol

This page is devoted to Content Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms..., that have been set-up to use Jmol as part of their contents.

Moodle

The Moodle filter for Jmol

Moodle is an open-source course management system. A third-party Jmol filter (information here and here) detects links to molecular model files (.mol, .csmol, .pdb, .xyz, .cml) in Moodle documents and converts them into embedded Jmol models. Jmol models can also be added as resources, or placed in searchable databases that students can edit.

Current version of the filter uses JSmol (the HTML5 modality, i.e. no Java) by default, unless a noncompatible system is detected.

Moodle sites using Jmol

If you know a Moodle which uses Jmol, and which is not in the list below, please add it.

• Yeovil College
• Monte Sant' Angelo Mercy College
• Frostburg State University
• Study (nano)materials at Technical University of Liberec (in Czech)

Molecular structures in Moodle

• How does the Jmol filter work?

Like the other text filters in Moodle, the Jmol filter expands a simple, shorthand code typed by an author into more complex code the browser can display. Specifically, this filter removes a link to a molecular file (with recognized file extension) and inserts a JmolApplet that loads the model. It can optionally insert controls too (e.g. for changing the rendering style).

• How do I embed molecules into Moodle pages?

First, make sure that the administrators of your Moodle site have installed the Jmol filter. Then, simply upload a .pdb file to your course, and make a link to it using Moodle's HTML editor.

The link must have title="Jmol" for it to work properly.

Note that the server must be the same for the uploaded file and the Moodle system files, since Jmol will not display remote pdb files.

<a href="?x=http://web.archive.orgpath/aspartic.pdb">Aspartic acid</a>

The default size of the display is 350 pixels. You can set the size of the display to n pixels by appending ?s=n to the URL. For example:

<a href="?x=http://web.archive.orgpath/aspartic.pdb?s=200">Aspartic acid</a>

You can turn the default controls off by appending ?c=0 to the URL. If you combine this with the sizing option, separate the parameters with an ampersand (&).

<a href="?x=http://web.archive.orgpath/aspartic.pdb?s=200&c=0">Aspartic acid</a>

For even greater control, pass a Jmol script to the view by typing JMOLSCRIPT{} after the link. The script goes between the braces.

For example, to set the background to white, zoom in to 150%, and spin the molecule around its x and y axes, you could type:

<a href="?x=http://web.archive.orgpath/aspartic.pdb?s=200&c=0">Aspartic acid</a>JMOLSCRIPT{color background white; zoom 150; set spin x 10; set spin y 10; spin;}

Internationalization

A project to internationalize the Jmol filter for Moodle was started on Jan 2008 [1]

A more recent update is including localization, i.e. translated text strings for different languages.

WebAssign

WebAssign® is a Course Management System offered as a service and done by North Carolina State University and Advanced Instructional Systems, Inc.

• Notice announcing Jmol functionality.

LON-CAPA

LON-CAPA is a "Free Open-Source Distributed Learning Content Management and Assessment System" under continuing development at Michigan State University. There are many exercises in the growing database of shared resources that use Jmol. Most require an account on the system to access the exercises, but a few are published "publicly" and do not require log-in for access. For example:

• a problem for lower grade science and math students
• assignment of R or S configuration
• structure comparison
• naming a structure
• comparing a 3D structure with a Fischer projection structure

Drupal

Drupal is an open source content management platform.

Drupal Jmol

A Drupal 7 module is available to display uploaded molecular structure files as a Jmol applet. The module can be found at http://drupal.org/project/jmol.

Drupal Molecule

Another Drupal module, called Molecule, enables to easily integrate JSmol and JSpecView objects into Drupal sites without technical knowledge. More information at the Molecule site

The Molecule module defines three types of display options for displaying JCAMP-DX files:

• Spectrum: Show the spectrum contained in the JCAMP-DX file
• Molecule: Show the molecule contained in the JCAMP-DX file
• Spectrum with molecule: Show both the molecule and the spectrum in the JCAMP-DX file and link them.

Mahara

The Mahara e-Portfolio system includes the 'Mahara artefact file blocktype jmol/jsmol plugin', which provides the interactive 3D display of chemical structure files, uploaded to Mahara, using Jmol/JSmol.

• Documentation
• Source code repository (GitHub)

Others

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