Jmol filter: Difference between revisions

Latest revision as of 19:54, 18 January 2016

An example of the Jmol filter in action

Jmol (Jsmol) is open-source software for interactive 3D viewing of chemical structures. It can easily be embedded into a webpage... including a Moodle page.

The Moodle Jmol filter makes it incredibly simple for teachers to embed these viewers into teaching material (quizzes, discussion messages, etc).

Download the Jmol filter for Moodle 2

Originally, Jmol was a developed as a Java applet, requiring no additional capability on your Web server, but requiring both Java and a JavaScript-enabled browser for the user.

More recently, the Jmol developers have created JSmol, an HTML5 canvas version of the Jmol applet that uses JavaScript. JSmol opens up the use of Jmol in PC, Mac, and Linux systems without Java installed or with Java disabled, as well as tablets and smart phones (both iOS and Android). No hardware-based graphics acceleration is used, allowing JSmol to run in any web browser that supports HTML5 standards.

JSmol allows rendering, scripting and interaction with the models just as Jmol does, since the source code is shared by both. Note that JSmol is not a different program to Jmol: it is Jmol, just compiled into JavaScript instead of Java (thanks to the Java2Script software).

In most circumstances, the Jmol filter defaults to using JSmol, the JavaScript/HTML5 version, for maximum cross-platform compatability.

If Internet Explorer 8 is used, the filter switches to the Jmol Java applet. Also, if certain chemical structure file-types (e.g. .pse or .pdb.zip) are used with browsers that don't fully support binary file-handling by JavaScript, the Jmol Java applet is also used.

Where the Java applet is required, recent versions of the filter use the self-signed applet, to minimise the security warnings/blocks generated by recent Java releases.

The Jmol filter is very useful for including a molecule viewer in a variety of situations - e.g. in a Label, a Forum discussion, or a Quiz question.

How to use

Upload a molecule data file to the Moodle server. (This is important - Jmol refuses to display data files held on other servers, so you can't just link to a file that exists somewhere else on the web.)
Simply create a link to the molecule file, wherever you want the molecule viewer to appear.

In more detail:

use the Moodle text editor (inside a course topic, label, HTML block, forum posting, quiz question etc) to add the text for a link, eg 'water'
click-and drag to select the text link
use the Insert Web Link button and enter the URL of the resource (already uploaded into the course's Files folder). The editor may 'scramble' things, particularly if you use additional parametes (below) and you may find it best to use HTML Source ([<>] button) view. So default usage of the Jmol filter, for a structure water.pdb, in course 7 of your.moodle.ac.uk might use the code:

<a title="Jmol" href="http://your.moodle.ac.uk/moodle/file.php/7/water.pdb">water</a>

Parameters can be added to the end of the URL to specify certain display options. Add ?c=0 to hide the controls, or ?s=150 to set the viewer's size at 150 pixels. Or ?c=0&s=150 to do both.

<a title="Jmol" href="http://your.moodle.ac.uk/moodle/file.php/7/water.pdb?c=0&s=150">water</a>

If you wish to run extra Jmol script upon intialisation, write JMOLSCRIPT{} straight after the link, and put your code inside the braces. For example:

<a title="Jmol" href="http://your.moodle.ac.uk/moodle/file.php/7/water.pdb">water</a>JMOLSCRIPT{rotate x 15; zoom 50; set axes on;}

The title tag is also essential for the filter to operate.

Jmol Help

@@ Line 1: / Line 1: @@
 [[Image:Jmol-quiz-example.png|thumb|200px|right|An example of the Jmol filter in action]]
-Jmol is open-source Java software for interactive 3D viewing of molecular structures. It can easily be embedded into a webpage... including a Moodle page.
+Jmol (Jsmol) is open-source software for interactive 3D viewing of chemical structures. It can easily be embedded into a webpage... including a Moodle page.
 The Moodle Jmol filter makes it incredibly simple for teachers to embed these viewers into teaching material (quizzes, discussion messages, etc).
-* '''[http://download.moodle.org/download.php/modules/filter_jmol.zip Download the Jmol filter]''''
+* '''[https://github.com/geoffrowland/moodle-filter_jmol Download the Jmol filter for Moodle 2]'''
-The Jmol filter is very useful for including a molecule viewer in a variety of situations - e.g. in a [[Label]], a [[Forums | Forum]] discussion, or a [[Quizzes| Quiz]] question. If you wish to load a molecule data file as a "resource", you should also consider installing the [[Jmol resource module]].
+Originally, Jmol was a developed as a Java applet, requiring no additional capability on your Web server, but requiring both Java and a JavaScript-enabled browser for the user.
+More recently, the Jmol developers have created JSmol, an HTML5 canvas version of the Jmol applet that uses JavaScript. JSmol opens up the use of Jmol in PC, Mac, and Linux systems without Java installed or with Java disabled, as well as tablets and smart phones (both iOS and Android). No hardware-based graphics acceleration is used, allowing JSmol to run in any web browser that supports HTML5 standards.
-It requires no additional capability on your web server, but requires both Java and a JavaScript-enabled browser for the user.
+JSmol allows rendering, scripting and interaction with the models just as Jmol does, since the source code is shared by both. Note that JSmol is not a different program to Jmol: it is Jmol, just compiled into JavaScript instead of Java (thanks to the Java2Script software).
-* [http://moodle.yeovil.ac.uk/course/view.php?id=63 See it in action in this course] (Log in as guest)
+In most circumstances, the Jmol filter defaults to using JSmol, the JavaScript/HTML5 version, for maximum cross-platform compatability.
+If Internet Explorer 8 is used, the filter switches to the Jmol Java applet. Also, if certain chemical structure file-types (e.g. .pse or .pdb.zip) are used with browsers that don't fully support binary file-handling by JavaScript, the Jmol Java applet is also used.
+Where the Java applet is required, recent versions of the filter use the self-signed applet, to minimise the security warnings/blocks generated by recent Java releases.
+The Jmol filter is very useful for including a molecule viewer in a variety of situations - e.g. in a [[Label]], a [[Forums | Forum]] discussion, or a [[Quizzes| Quiz]] question.
@@ Line 19: / Line 26: @@
 # Upload a molecule data file to the Moodle server. (This is important - Jmol refuses to display data files held on other servers, so you can't just link to a file that exists somewhere else on the web.)
 # Simply create a link to the molecule file, wherever you want the molecule viewer to appear.
-##In more detail:
+====In more detail:====
-** use the Moodle text editor to add the text for a link, eg 'water'
+* use the Moodle text editor (inside a course topic, label, HTML block, forum posting, quiz question etc) to add the text for a link, eg 'water'
-** click-and drag to select the text link
+* click-and drag to select the text link
-** use the Add Web link button and entere the URL of the resource (already uploaded into the course's Files folder). The editor may 'scramble' things, particularly if you use additional parametes (below) and you may find it best to use HTML Source ([<>] button) view. So default usage of the Jmol filter, for a structure water.pdb, in course 7  of your.moodle.ac.uk might use the code:
+* use the Insert Web Link button and enter the URL of the resource (already uploaded into the course's Files folder). The editor may 'scramble' things, particularly if you use additional parametes (below) and you may find it best to use HTML Source ([<>] button) view. So default usage of the Jmol filter, for a structure water.pdb, in course 7  of your.moodle.ac.uk might use the code:
   <a title="Jmol" href="http://your.moodle.ac.uk/moodle/file.php/7/water.pdb">water</a>
-## Parameters can be added to the end of the URL to specify certain display options. Add '''?c=0''' to hide the controls, or '''?s=150''' to set the viewer's size at 150 pixels. Or '''?c=0&s=150''' to do both.
+* Parameters can be added to the end of the URL to specify certain display options. Add '''?c=0''' to hide the controls, or '''?s=150''' to set the viewer's size at 150 pixels. Or '''?c=0&s=150''' to do both.
   <a title="Jmol" href="http://your.moodle.ac.uk/moodle/file.php/7/water.pdb?c=0&s=150">water</a>
+* If you wish to run extra [http://jmol.sourceforge.net/scripting/ Jmol script] upon intialisation, write '''JMOLSCRIPT{}''' straight after the link, and put your code inside the braces. For example:
-## The filter will output its own form tags. If you're displaying the molecule inside an existing form, please make sure you use the '''?f=0''' parameter to make sure the filter doesn't output its own form tags. This will ensure things work correctly in most web browsers.
-# If you wish to run extra [http://jmol.sourceforge.net/scripting/ Jmol script] upon intialisation, write '''JMOLSCRIPT{}''' straight after the link, and put your code inside the braces. For example:
   <a title="Jmol" href="http://your.moodle.ac.uk/moodle/file.php/7/water.pdb">water</a>JMOLSCRIPT{rotate x 15; zoom 50; set axes on;}
-===Important: Using the filter in quizzes===
+The title tag is also essential for the filter to operate.
-The filter can be used to display molecular viewers in quiz questions. But '''please make sure you use the ?f=0 parameter at the end of each URL''', to prevent the filter outputting its own "form" tags.
+[[Jmol Help]]
-[[Category:Administrator]]
+[[Category:Contributed code]]
 [[Category:Filter]]
+[[Category:Chemistry]]
+[[es:Filtro Jmol]]

Documentation

Jmol filter: Difference between revisions

Latest revision as of 19:54, 18 January 2016

How to use

In more detail: