CMS Using Jmol
- Websites Using J(S)mol
- J(S)mol in the Classroom
- Journals Using J(S)mol
- J(S)mol Literature
- Articles Using J(S)mol
- Books Using J(S)mol
- Wikis Using J(S)mol
- Blogs Using J(S)mol
- CMS Using J(S)mol (Moodle and others)
Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms - Applications Embedding Jmol
- Distributions Including Jmol
- Blue Obelisk
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.
Contents
OpenOChem
OpenOChem is an advanced homework/quizzing system that plugs in existing Learning Management Systems via Learning Tools Interoperability® (LTI) specification. There is a 3D model kit based on JSmol
Moodle
Moodle is an open-source course management system.
Molecular model files may be displayed in Moodle pages using a filter, a resource, or placed in searchable databases that students can edit.
Compatibility with recent Moodle versions is uncertain; if you have installed this filter or resource in your Moodle, please contact us[1] with information that might be added here.
The Jmol filter for Moodle
A third-party Jmol filter (information) detects links to molecular model files (.mol, .csmol, .pdb, .xyz, .cml) in Moodle documents and converts them into embedded Jmol models.
Current version of the filter uses by default JSmol_HTML5 (i.e. Java is not used). The user can also opt for the JSmol_WebGL modality.
- Download v.6.5 for Moodle 3.6 to 3.8 at least
- Download v.6.4 for Moodle 2.x and 3.x
- Download older versions of the the Jmol filter (e.g. for Moodle 1.8 and 1.9)
This is a snapshot of a model inserted in a page using this filter (Moodle v.3.5.2, Jmol Filter v.6.1):
Inserting molecular models
- 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 converting it into more complex code the browser can display. Specifically, this filter removes a link to a molecular structure file (with recognized file extension) and inserts a JSmol panel 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?
- Config: First, make sure that the administrators of your Moodle site have installed the Jmol filter.
- Upload files: Then, simply upload to your course a molecular structure file and make a link to it using Moodle's HTML editor.
- Formats of molecular structure that are recognized as such, based on the file extension (variable
$jmolfiletypesin the filter source code):
- Formats of molecular structure that are recognized as such, based on the file extension (variable
mol sdf mol2 xyz cml cif mcif pdb csmol jmol pse mol.png sdf.png mol2.png xyz.png cml.png cif.png mcif.png pdb.png csmol.png jmol.png pse.png pdb.gz
- (png files must be PNGJ files generated by Jmol)
- Note that the server must be the same for the uploaded file and the Moodle system files, since Jmol will not display remote files.
- Link: Insert a link in <a href="path/aspartic.pdb">Aspartic acid</a> The link must have
- Options:
- The default size of the display is 350 pixels. You can set the size of the display to n pixels by appending
?s=nto the URL. For example:
- The default size of the display is 350 pixels. You can set the size of the display to n pixels by appending
title="Jmol" for it to work properly.
<a href="path/aspartic.pdb?s=200">Aspartic acid</a>
- You can turn the default controls off by appending
?c=0to the URL. If you combine this with the sizing option, separate the parameters with an ampersand (&).
- You can turn the default controls off by appending
<a href="path/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 even greater control, pass a Jmol script to the view by typing
- 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="path/aspartic.pdb?s=200&c=0">Aspartic acid</a>JMOLSCRIPT{color background white; zoom 150; set spin x 10; set spin y 10; spin;}
The Jmol resource for Moodle
Jmol models can also be added as resources.
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)
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 and 8 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. It is only development version, last updated in 2015.
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)
WordPress
For open source content management system WordPress there is a jsmol2wp plugin, that has been closed as of January 7, 2019 and is not available for download for security issue.
Others
...?
- ↑ jmol-developers AT lists.sourceforge.net
Contributors
AngelHerraez, Jvdurme, Martin.slavik, Fsenese, NicolasVervelle, Pimpim, Vinnystocker
