Difference between revisions of "CMS Using Jmol"

From Jmol
Jump to navigation Jump to search
(username removed)
(→‎Moodle)
 
(36 intermediate revisions by 4 users not shown)
Line 2: Line 2:
  
 
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.
 
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.
 +
 +
== OpenOChem ==
 +
[http://openochem.org/ooc/ OpenOChem] is an advanced homework/quizzing system that plugs in existing Learning Management Systems via Learning Tools Interoperability® (LTI) specification. There is a [http://openochem.org/tsugi/store/details/jsmolmodels 3D model kit based on JSmol]
  
 
== Moodle ==
 
== Moodle ==
−
=== Moodle sites using Jmol ===
+
[http://moodle.org/ Moodle] is an open-source course management system.  
−
[http://moodle.org/ Moodle] is an open-source course management system. A third-party '''Jmol filter''' ([http://docs.moodle.org/en/Jmol_filter info]) automatically converts links to molecular model files (.mol, .csmol, .pdb, .xyz, .cml) in Moodle documents into embedded Jmol models. Jmol models can also be added as [http://moodle.org/mod/data/view.php?d=13&rid=87 resources], or placed in searchable databases that students can edit.
+
 
 +
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<ref name="DevList">Send an email to mol-developers AT lists DOT sourceforge DOT net</ref> with information that might be added here.
 +
 
 +
=== The Jmol filter for Moodle ===
 +
A third-party '''Jmol filter'''<ref name="MoodleDocs">[https://docs.moodle.org/36/en/Jmol_filter Official page for the Jmol filter at MoodleDocs]</ref> detects links to molecular model files (.mol, .pdb, .xyz, .cml, ...) in Moodle pages and converts them into embedded JSmol models.  
 +
 
 +
Current version of the filter uses by default [[Jmol_JavaScript_Object|'''JSmol_HTML5''']] (i.e. Java is not used). The user can also opt for the [[Jmol_JavaScript_Object/WebGL|'''JSmol_WebGL''' modality]].
 +
 
 +
{| class="wikitable"
 +
|-
 +
! Moodle version !! 
 +
|-
 +
| Moodle 4.5 || Needs a new architecture for the filter. [https://github.com/geoffrowland/moodle-filter_jmol/issues/40 Discussion]
 +
|-
 +
| Moodle 4.1 || [https://github.com/jpahullo/moodle-filter_jmol Code and download] v.6.4, build 2024012000
 +
|-
 +
| Moodle 3.6 to 3.8 || [https://edugit.org/nik/moodle-filter_jmol Code and download] v.6.4, Build 2016050100 (modified 20161118)
 +
|-
 +
| Moodle 2.x and 3.x || [https://github.com/geoffrowland/moodle-filter_jmol Code and download] v.6.4, Build 2016050100
 +
|-
 +
| Moodle 1.8 and 1.9 || [https://github.com/geoffrowland/moodle-filter_jmol/tree/MOODLE_19_STABLE Code and download] older versions of the Jmol filter
 +
|}
 +
 
 +
Example:[[File:Moodle Filter.png|frame|center|This is a snapshot of a model inserted in a page using this filter (Moodle v.3.5.2, Jmol Filter v.6.1)]]
  
−
If you know a Moodle which uses Jmol, and which is not in the list below, please add it.
+
==== How to insert molecular models in a Moodle page ====
 
<!--
 
<!--
−
* [http://www.reviseguys.com/moodle/course/view.php?id=2 reviseguys Chemistry revision]
+
[http://marie.frostburg.edu/101/mod/wiki/view.php?id=787&page=Index Moodle FAQ at  Frostburg State University] explains briefly
 +
This link is dead, but there is a 2006 version in Web Archive. I'm pasting here the significant bits.
 
-->
 
-->
−
* [http://moodle.yeovil.ac.uk/course/view.php?id=63 Yeovil College]
+
* How does the Jmol filter work?
−
* [http://montenet.monte.nsw.edu.au/ Monte Sant' Angelo Mercy College]
+
: 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 that is displayed by the browser. Specifically, this filter removes a link to a file (with molecular structure data, recognized by its extension) and inserts a JSmol panel that loads the model. It can optionally insert controls too (e.g. for changing the rendering style).
−
* [http://confchem.frostburgchemistry.org Frostburg State University]
+
:: ''Note for wiki administrators: authorization to upload those types of files may be needed in the wiki configuration.''
−
* [http://moodle.fp.tul.cz/course/view.php?id=208 Technical University of Liberec (in Czech)]
+
* How do I embed molecules into Moodle pages?
 +
# '''Config:''' First, make sure that the administrators of your Moodle site have installed the Jmol filter and authorized upload of such file extensions.
 +
# '''Upload file:''' 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 <code>$jmolfiletypes</code> in the filter source code), are:
 +
::{| class="wikitable"
 +
|-
 +
| 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 [[File_formats/Compressed|PNGJ]] files generated by Jmol, containing both a snapshot image and the structural data)
 +
:: ''Note that the server must be the same for the uploaded file and the Moodle system files; JSmol will not display remote files.''
 +
# <li value="3">'''Link:''' Use the Moodle text editor (inside a course topic, label, HTML block, forum posting, quiz question, etc.) to add the text for a link, e.g. 'Aspartic acid'. Click and drag to select the text link. Use the ''Insert Web Link'' button and enter the URL of the structure file. Note that the editor may 'scramble' things, particularly if you use additional parameters (explained in 'Options' below), so you may find it best to use ''HTML Source view'' ([<>] button). The result could be like this: <code><a title="Jmol" href="http://someserver.edu/moodle/file.php/7/Asp.mol">Aspartic acid</a></code>. '''Important:''' the link must have <code>title="Jmol"</code> for it to work properly.
 +
# '''Options:'''
 +
#* The default size of the display is 350 pixels. You can set it to ''n'' pixels by appending <code>?s=n</code> to the URL: <code><a href="path/Asp.mol?s=200">Aspartic acid</a></code>  The user can anyway resize the viewer dragging the bottom-right corner, or click a toggle button to display the viewer full-screen. When more than one parameter is used in the URL, they are separated with an ampersand (&).
 +
#* You can specify whether the controls under the viewer are included by appending <code>?c=n</code> to the URL: <code><a href="path/Asp.mol?s=200&c=0">Aspartic acid</a></code>:
 +
#** <code>?c=0</code> to hide the controls.
 +
#** <code>?c=1</code> to display controls suitable for small inorganic or organic chemical structures.
 +
#** <code>?c=2</code> to display instead crystallographic controls for display of unit cells, crystal packing and polyhedra (for data files that support these).
 +
#** <code>?c=3</code> to use controls suitable for biological macromolecules such as proteins or nucleic acids.
 +
#** The default is to show controls according to the type of file loaded (c=3 for pdb, c=2 for cif).
 +
#* You can also specify whether the initial display is the interactive structure (<code>?i=0</code>) (default) or it is a cover image, replaced by the interactive object upon user click (<code>?i=1</code>), giving faster page load.
 +
#* For even greater control, pass a Jmol script to the view by typing <code>JMOLSCRIPT{}</code> right after the link. The script goes between the braces. <code><a href="path/Asp.mol?s=200&c=0">Aspartic acid</a>JMOLSCRIPT{color background white; zoom 150; set spin x 10; set spin y 10; spin on;}</code> will set the background to white, zoom in to 150%, and spin the molecule around its X and Y axes at 10 degrees per second.
  
−
=== Molecular structures in Moodle ===
+
:''Credits: A good part of this explanation was copied from the Moodle FAQ at Frostburg State University<ref>[https://web.archive.org/web/20250000000000*/http://marie.frostburg.edu/101/mod/wiki/view.php?id=787&page=Index Archived copy of http://marie.frostburg.edu/101/mod/wiki/view.php?id=787&page=Index] </ref>'' combined with MoodleDocs<ref name="MoodleDocs"></ref>
−
[http://marie.frostburg.edu/101/mod/wiki/view.php?id=787&page=Index Moodle FAQ at  Frostburg State University] explains briefly
+
 
−
* How do I embed molecules into Moodle pages?
+
=== The Jmol resource for Moodle ===
−
* How does the Jmol text filter work?
+
Jmol models can also be added as ''Moodle resources''<ref>[https://docs.moodle.org/20/en/Jmol_resource_type Jmol resource type]</ref>.
−
* How can I display .mol files in Moodle?
 
  
 +
<!--
 +
=== Moodle sites using Jmol ===
 +
If you know a Moodle which uses Jmol, and which is not in the list below, please add it.
 +
    * [http://www.reviseguys.com/moodle/course/view.php?id=2 reviseguys Chemistry revision]
 +
* [https://moodle.yeovil.ac.uk/ Yeovil College]
 +
* [https://www.monte.nsw.edu.au/ Monte Sant' Angelo Mercy College]
 +
* [https://confchem.ccce.divched.org/2006SpringConfChemP8B Frostburg State University]
 +
* [https://nanoed.tul.cz/course/view.php?id=86 Study (nano)materials at Technical University of Liberec (in Czech)]
 +
-->
 
=== Internationalization ===
 
=== Internationalization ===
−
The Jmol filter for Moodle is being internationalized (Jan 2008) [http://code.google.com/p/google-highly-open-participation-moodle/issues/detail?id=78]
+
A project to internationalize the Jmol filter for Moodle was started on Jan 2008.<ref>http://code.google.com/p/google-highly-open-participation-moodle/issues/detail?id=78</ref>
−
 
+
A more recent update is including localization, i.e. translated text strings for different languages.
 +
Both are apparently included in the latest versions of the filter (<code>lang</code> folder), although some languages may need an update to fully match the collection of text strings in English.
  
 
== WebAssign ==
 
== WebAssign ==
−
[http://webassign.net/index.html WebAssign®] is a Course Management System offered as a service and done by North Carolina State University and Advanced Instructional Systems, Inc.  
+
[http://webassign.net/index.html WebAssign®] is a Course Management System offered as a service and done by North Carolina State University and Advanced Instructional Systems, Inc.  
 
* [http://webassign.net/info/announcements/2005_7_8.html Notice] announcing Jmol functionality.
 
* [http://webassign.net/info/announcements/2005_7_8.html Notice] announcing Jmol functionality.
−
 
  
 
== LON-CAPA ==
 
== LON-CAPA ==
Line 43: Line 104:
 
[http://drupal.org/ Drupal] is an open source content management platform.
 
[http://drupal.org/ Drupal] is an open source content management platform.
  
−
Compatibility with Jmol is uncertain yet; this needs to be documented.
+
=== 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 http://drupal.org/project/jmol].
  
−
== Others ==
+
=== Drupal Molecule ===
−
[http://www.crushersolution.com/crusher/crusher.html Crusher] has full names of stone crusher, rock crusher, quarry crusher widely applied in stone quarry plants, [http://www.millexpert.com/blog/category/equipment mining equipment] industry, ore crushing plants, building and construction, highway, railway, water conservancy and chemical industry etc. Depending on the crushing stage, we can divide crushers into four models: mobile crusher, primary crusher, secondary crusher, tertiary crusher. The primary crusher mainly refers to the [http://www.usedjawcrusher.com jaw crusher] and impact crusher. In the designing of a crushing plant of any nature and size, to select the right type and size of primary crusher is of great significance. Generally speaking, this machine is the largest and most expensive single item in the plant; a mistake in the choice may lead to a full replacement. Therefore, you have to pay close attention when choosing primary crushers. The following tips may be helpful for the selection of primary crushers.
+
Another Drupal module, called '''Molecule''', enables to easily integrate JSmol and JSpecView objects into Drupal sites without technical knowledge. More information at the [http://www.drupal.org/project/molecule Molecule site]. It is only development version, last updated in 2015.  
−
== [http://www.millexpert.com/blog/jaw-crusher/ Jaw crusher] introduction ==
 
  
−
[http://www.crushersolution.com/crusher/jaw-crusher.html Jaw crusher], also named jaw [http://www.crushersolution.com/products.html crushing machine] or jaw breaker is the world's most ancient form of [http://www.millexpert.com stone crusher] or rock crusher. Jaw crusher's main part is jaw crushing chamber composed of dynamic crusher jaw and static crusher [http://www.millexpert.com/blog/jaw-crusher/ jaw crusher] simulating jaw movement of animals to complete the stone material crushing operations.  
+
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.
  
−
== [http://www.millexpert.com/crusher/hammer-crusher.html Hammer Crusher] Introduction ==
 
  
−
[http://www.crushersolution.com/crusher/hammer-crusher.html Hammer crusher] also named hammer mill is used for crushing all kinds of abrasive weak materials or mid-hardness stone. The materials crushed by hammer crusher such as coal, salt, chalk, gypsum, brick, limestone and so on with compressive strength not exceed 100MPa, and water content range less than 15%. Hammer crusher also can be used for crushing used wood, paper, asbestos cement’s wastes with fiber structure, strong flexibility etc to recover asbestos fibers.
+
== 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.
 +
* [https://wiki.mahara.org/wiki/Plugins/Blocktype/Jmol Documentation]
 +
* [https://github.com/geoffrowland/mahara-artefact_file_blocktype_jmol Source code repository] (GitHub)
  
−
== [http://www.millexpert.com/crusher/impact-crusher.html Impact Crusher] Introduction ==
+
== WordPress ==
−
[http://www.crushersolution.com/crusher/impact-crusher.html Impact crusher] is new highly efficient [http://www.minecrusher.com crushing equipment] which is ideal choice for [http://www.crushersolution.com/solution/crusher-solution.html crushing and screening] in stone production line or rock [http://www.millexpert.com/crushing-plant/crushing-plant.html crushing plants]. Impact [http://www.millexpert.com/blog/category/crusher crusher] can crush stone in selective methods and it’s a promising device in mining, transportation, energy, construction and chemical industry.
+
For open source content management system [https://wordpress.org/ WordPress] there is a [https://wordpress.org/plugins/jsmol2wp/ jsmol2wp plugin], that has been closed as of January 7, 2019 and is not available for download for security issue.
  
−
== [http://www.millexpert.com/crusher/symons-cone-crusher.html Symons Cone Crusher] Introduction ==
+
== Others ==
−
 
+
...?
−
[http://www.crushersolution.com/crusher/symons-cone-crusher.html Symons cone crusher] was the world’s first [http://www.aconecrusher.com cone crusher] which is now widely used in metallurgy, construction, chemicals, building materials processing industry. Symons cone crusher has improved from traditional cone [http://www.millexpert.com/blog/products/ crusher] by SBM adopting domestic and international design experience so that this cone crusher has excellent performance in the manufacture, installation, use and maintenance etc.
 
−
 
 
−
== [http://www.millexpert.com/blog/mobile-crusher/ Mobile crusher] Introduction ==
 
−
 
 
−
[http://www.crushersolution.com/crusher/mobile-crusher.html Mobile crusher] also called portable crusher is a [http://www.grindercrusher.com stone crusher] that is easy to move before crushing or after crushing process. [http://www.millexpert.com/blog/category/mobile-crusher-2 Mobile crusher] for sale in China, the first choice of mobile crusher station is SBM. According to the capacity and crusher weight, we can divide mobile crusher into small [http://www.mobilecrusherglobal.com mobile crusher] (mini mobile crusher) and heavy duty mobile crusher.
 
−
 
 
−
SBM, a professional mobile [http://www.crushersolution.com/crusher-application/crusher-application.html crusher] manufacturer or mobile crusher supplier can supply you five models mobile [http://www.millexpert.com/crusher/crusher.html crusher]: jaw crusher series mobile crusher, cone crusher series mobile crusher, [http://www.crushersolution.com/crusher-application/mobile-impact-crusher.html impact crusher series mobile crusher], multi-crushing type mobile crusher and crawler type mobile crusher etc.
 
−
 
 
−
[http://www.crushersolution.com/grinding-mill/grinding-mill.html Grinding mill] also named [http://www.grindingmill.net grinder mill], grinding machine, grinder equipment, grinding equipment etc includes ball grinding mill, Raymond grinding mill, vertical grinding mill, trapezium grinding mill, coarse powder grinding mill, high pressure suspension grinding mill, etc..
 
−
 
 
−
== [http://www.millexpert.com/grinding-mill/ball-mill.html Ball mill] Introduction ==
 
−
 
 
−
[http://www.crushersolution.com/grinding-mill/ball-mill.html Ball mill] also named ball roller [http://www.millexpert.com/blog/category/grinder-mill grinder mill], ball grinder mill is a cylindrical device used for grinding materials with low hardness such as limestone, cement, raw coal etc. According to ball mill specifications, SBM ball mill widely applied to grind varies ores and grind-able raw materials in dry grinding and wet grinding.
 
−
 
 
−
== [http://www.millexpert.com/grinding-mill/raymond-mill.html Raymond mill] Introduction ==
 
−
 
 
−
[http://www.crushersolution.com/grinding-mill/raymond-mill.html Raymond mill] or Raymond grinder is a grinding machine from abroad with long history and advanced technology. Raymond mill technology has applied to many traditional grinder machines such as Raymond ball mill, Raymond vertical mill, Raymond coal mill, Raymond roller mill etc. It has widely used in mines, cement plants, chemical plants as a grinding equipments. And Raymond mill is key equipment in non-metallic mineral processing plants.
 
−
 
 
−
== [http://www.millexpert.com/grinding-mill/vertical-mill.html Vertical mill] Introduction ==  
 
−
 
 
−
[http://www.crushersolution.com/grinding-mill/vertical-mill.html Vertical mill] also named vertical grinder mill, vertical grinding machine, vertical milling machine; and vertical roller mill etc adopts advanced grinding technology and combines with various grinder mill machines producing experience. Vertical mill is a set of equipment combined with crushing, drying, grinding, grading and transporting etc.
 
−
 
 
−
== [http://www.millexpert.com/blog/quarry-crusher-fatality.html Quarry Crusher] Introduction ==
 
−
 
 
−
The [http://www.crushersolution.com/solution/quarry-crusher.html quarry crusher], also known as [http://www.millexpert.com/blog/primary-crusher.html stone crusher], is mainly applied in various construction projects for crushing large stones into smaller particle sizes. Our company, as a professional crusher manufacturer, specializes in producing various types of crushing machines. Generally speaking, the quarry crushers can be divided into three major types, that is, [http://www.millexpert.com/crusher/jaw-crusher.html jaw crusher], roller crusher and [http://www.millexpert.com/crusher/hydraulic-cone-crusher.html cone crusher]. [http://www.usedjawcrusher.com Jaw crushers] crush rock by closing two walls against the large stones several times. Cone crushers crush rock through spinning grinders. Roller crushers are often used for [http://www.crushersolution.com/solution/crusher-solution.html secondary crushing]; rocks are fed between two rollers that crush the rock.
 
−
 
 
−
== [http://www.orecrusher.net Ore Crusher] Introduction ==
 
−
The most commonly used crushers and grinding mills in iron ore crushing and grinding process for iron ore mining are jaw crusher, cone crusher, hammer crusher and ball mill, ultrafine grinding mill, etc. In iron ore mining, miner usually choose a complete iron ore crushing plant for metallurgy. At present, the most popular iron ore production line consists of two jaw crushers. After beening crushed, the material will be transported for the magnetic separation, and then into the ball mill for grinding.
 
−
 
 
−
== [http://www.gravelcrusher.net Gravel Crusher] Introduction ==
 
−
Jaw gravel crusher for iron ore: [http://www.crushersolution.com Jaw crusher] is used in primary crushing station. It can crush iron ore into small sizes. Thus, these small iron ore can enter into the iron ore mill such as ball mill for grinding.
 
−
 
 
−
Impact gravel crusher is generally used after jaw [http://www.crushersolution.com/project-case/project-case.html crusher], and can crush hard stones, not only the iron ore, but also other ores such as copper, bauxite, gold, Kaolinite, manganese etc.
 
−
 
 
−
Hammer gravel crushers are widely used in small quarries with small capacities. That's because in such situation, the cost and the difficulty of changing and maintaining worn hammers are more acceptable to the quarry owners. However, once the quarry owners want to enhance the capacity to above 50-60t/h by one [http://www.millexpert.com crushing plant], hammer crushers are no longer suitable. Using hammer crusher to do a big crushing work will lead to a passive situation of high consuming cost and frequent maintenance.
 
−
 
 
−
Cone gravel crusher is the most common fine iron [http://www.crushersolution.com/solution/rock-crusher.html ore crusher machine], and usually used as final iron ore crushing machine. It has four types: spring cone crusher, symons cne crusher, hydraulic cone crusher, hcs90 cone crusher. Every cone crusher has their different applications.
 
−
 
 
−
== [http://www.vibratingfeederchina.com Vibrating Feeder] Introduction ==
 
−
Vibrating feeder is the machine used to feed iron ore evenly to iron ore crushing and grinding machine in iron ore processing plant.
 
  
−
Vibrating screen is the screening machine used in iron ore [http://www.crushersolution.com/solution/mining-equipment.html crushing and screening plant]. It screens out the appropriate iron ore particles, these particles enter into ball mill for grinding.
+
== References ==
 +
<references />

Latest revision as of 12:44, 27 January 2025

Jmol / JSmol Applications

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.

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[2] detects links to molecular model files (.mol, .pdb, .xyz, .cml, ...) in Moodle pages and converts them into embedded JSmol 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.

Moodle version
Moodle 4.5 Needs a new architecture for the filter. Discussion
Moodle 4.1 Code and download v.6.4, build 2024012000
Moodle 3.6 to 3.8 Code and download v.6.4, Build 2016050100 (modified 20161118)
Moodle 2.x and 3.x Code and download v.6.4, Build 2016050100
Moodle 1.8 and 1.9 Code and download older versions of the Jmol filter

Example:

This is a snapshot of a model inserted in a page using this filter (Moodle v.3.5.2, Jmol Filter v.6.1)

How to insert molecular models in a Moodle page

  • 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 that is displayed by the browser. Specifically, this filter removes a link to a file (with molecular structure data, recognized by its extension) and inserts a JSmol panel that loads the model. It can optionally insert controls too (e.g. for changing the rendering style).
Note for wiki administrators: authorization to upload those types of files may be needed in the wiki configuration.
  • How do I embed molecules into Moodle pages?
  1. Config: First, make sure that the administrators of your Moodle site have installed the Jmol filter and authorized upload of such file extensions.
  2. Upload file: 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 $jmolfiletypes in the filter source code), are:
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, containing both a snapshot image and the structural data)
Note that the server must be the same for the uploaded file and the Moodle system files; JSmol will not display remote files.
  2. Link: Use the Moodle text editor (inside a course topic, label, HTML block, forum posting, quiz question, etc.) to add the text for a link, e.g. 'Aspartic acid'. Click and drag to select the text link. Use the Insert Web Link button and enter the URL of the structure file. Note that the editor may 'scramble' things, particularly if you use additional parameters (explained in 'Options' below), so you may find it best to use HTML Source view ([<>] button). The result could be like this: <a title="Jmol" href="http://someserver.edu/moodle/file.php/7/Asp.mol">Aspartic acid</a>. Important: the link must have title="Jmol" for it to work properly.
  3. Options:
    • The default size of the display is 350 pixels. You can set it to n pixels by appending ?s=n to the URL: <a href="path/Asp.mol?s=200">Aspartic acid</a> The user can anyway resize the viewer dragging the bottom-right corner, or click a toggle button to display the viewer full-screen. When more than one parameter is used in the URL, they are separated with an ampersand (&).
    • You can specify whether the controls under the viewer are included by appending ?c=n to the URL: <a href="path/Asp.mol?s=200&c=0">Aspartic acid</a>:
      • ?c=0 to hide the controls.
      • ?c=1 to display controls suitable for small inorganic or organic chemical structures.
      • ?c=2 to display instead crystallographic controls for display of unit cells, crystal packing and polyhedra (for data files that support these).
      • ?c=3 to use controls suitable for biological macromolecules such as proteins or nucleic acids.
      • The default is to show controls according to the type of file loaded (c=3 for pdb, c=2 for cif).
    • You can also specify whether the initial display is the interactive structure (?i=0) (default) or it is a cover image, replaced by the interactive object upon user click (?i=1), giving faster page load.
    • For even greater control, pass a Jmol script to the view by typing JMOLSCRIPT{} right after the link. The script goes between the braces. <a href="path/Asp.mol?s=200&c=0">Aspartic acid</a>JMOLSCRIPT{color background white; zoom 150; set spin x 10; set spin y 10; spin on;} will set the background to white, zoom in to 150%, and spin the molecule around its X and Y axes at 10 degrees per second.
Credits: A good part of this explanation was copied from the Moodle FAQ at Frostburg State University[3] combined with MoodleDocs[2]

The Jmol resource for Moodle

Jmol models can also be added as Moodle resources[4].

Internationalization

A project to internationalize the Jmol filter for Moodle was started on Jan 2008.[5] A more recent update is including localization, i.e. translated text strings for different languages. Both are apparently included in the latest versions of the filter (lang folder), although some languages may need an update to fully match the collection of text strings in English.

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:


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.

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

...?

References

  1. ↑ Send an email to mol-developers AT lists DOT sourceforge DOT net
  2. ↑ 2.0 2.1 Official page for the Jmol filter at MoodleDocs
  3. ↑ Archived copy of http://marie.frostburg.edu/101/mod/wiki/view.php?id=787&page=Index
  4. ↑ Jmol resource type
  5. ↑ http://code.google.com/p/google-highly-open-participation-moodle/issues/detail?id=78

Contributors

AngelHerraez, Jvdurme, Martin.slavik, Fsenese, NicolasVervelle, Pimpim, Vinnystocker

Retrieved from "https://wiki.jmol.org/index.php?title=CMS_Using_Jmol&oldid=10375"