CMS Using Jmol - Revision history

AngelHerraez: /* The Jmol filter for Moodle */

2025-01-31T16:09:55Z

‎The Jmol filter for Moodle

AngelHerraez: /* Moodle */

2025-01-27T12:44:06Z

‎Moodle

AngelHerraez: add heading for references section

2025-01-27T11:58:01Z

add heading for references section

AngelHerraez: /* Moodle */

2025-01-25T20:39:16Z

‎Moodle

AngelHerraez: /* Moodle */

2025-01-25T15:58:14Z

‎Moodle

AngelHerraez: /* Moodle */

2025-01-25T15:50:15Z

‎Moodle

AngelHerraez: /* Moodle */

2025-01-25T13:28:36Z

‎Moodle

AngelHerraez: /* Inserting molecular models */

2025-01-25T13:25:22Z

‎Inserting molecular models

AngelHerraez: /* The Jmol filter for Moodle */

2025-01-25T12:31:28Z

‎The Jmol filter for Moodle

AngelHerraez: Jmol filter for Moodle 3.6

2025-01-24T19:46:22Z

Jmol filter for Moodle 3.6

@@ Line 22: / Line 22: @@
 ! Moodle version !!
 |-
-| Moodle 4.5 || Needs a new architecture for the filter. [https://github.com/geoffrowland/moodle-filter_jmol/issues/40 Discussion]
+| Moodle 4.5 || Change to a new code architecture for the filter. [https://github.com/geoffrowland/moodle-filter_jmol/issues/40 Discussion] [https://github.com/jpahullo/moodle-filter_jmol Code and download] v.6.4, build 20254012000 (Unofficial)
 |-
-| Moodle 4.1 || [https://github.com/jpahullo/moodle-filter_jmol Code and download] v.6.4, build 2024012000
+| Moodle 3.6 to 3.8 (to 4.4?) || [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
@@ Line 49: / Line 47: @@
 ::{| class="wikitable"
 |-
-| mol || sdf || mol2 || xyz || cml || cif || mcif || pdb || csmol || jmol || pse
+| mol || sdf || mol2 || xyz || cml || cif || mcif || pdb || jmol || pse
 |-
-| mol.png || sdf.png || mol2.png || xyz.png || cml.png || cif.png || mcif.png || pdb.png || csmol.png || jmol.png || pse.png
+| mol.png || sdf.png || mol2.png || xyz.png || cml.png || cif.png || mcif.png || pdb.png || jmol.png || pse.png
 |-
 |  ||  ||  ||  ||  ||  ||  || pdb.gz ||  ||  ||

@@ Line 18: / Line 18: @@
 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]].
-* [https://edugit.org/nik/moodle-filter_jmol Download] v.6.5 for Moodle 3.6 to 3.8 at least
+{| class="wikitable"
-* [https://github.com/geoffrowland/moodle-filter_jmol Download] v.6.4 for Moodle 2.x and 3.x
+|-
-* [https://github.com/geoffrowland/moodle-filter_jmol/tree/MOODLE_19_STABLE Download] older versions of the the Jmol filter (e.g. for Moodle 1.8 and 1.9)
+! Moodle version !!
 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)]]

@@ Line 114: / Line 114: @@
 == WordPress ==
 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.
 == Others ==
 ...?

@@ Line 14: / Line 14: @@
 === 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 documents and converts them into embedded JSmol models.
+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]].
@@ Line 22: / Line 22: @@
 * [https://github.com/geoffrowland/moodle-filter_jmol/tree/MOODLE_19_STABLE 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):
+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)]]
 ==== How to insert molecular models in a Moodle page ====
@@ Line 31: / Line 30: @@
 -->
 * 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).
+: 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).
 * How do I embed molecules into Moodle pages?
-# '''Config:''' First, make sure that the administrators of your Moodle site have installed the Jmol filter.
+# '''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>$jmolfiletypes</code> in the filter source code):
+::  Formats of molecular structure that are recognized as such, based on the file extension (variable <code>$jmolfiletypes</code> in the filter source code), are:
 ::{| class="wikitable"
 |-
@@ Line 44: / Line 44: @@
 |  ||  ||  ||  ||  ||  ||  || pdb.gz ||  ||  ||
 |}
-:: (png files must be [[File_formats/Compressed|PNGJ]] files generated by Jmol)
+:: (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, since Jmol will not display remote files.
+:: ''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 (below), so you may find it best to use HTML Source ([<>] button) view. 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.
+# <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 (&).
@@ Line 55: / Line 55: @@
 #** <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 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.
+#* 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> 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.
+#* 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.
 :''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>
@@ Line 72: / Line 72: @@
 * [https://nanoed.tul.cz/course/view.php?id=86 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 <ref>http://code.google.com/p/google-highly-open-participation-moodle/issues/detail?id=78</ref>
+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.
 == WebAssign ==

@@ Line 25: / Line 25: @@
 [[File:Moodle Filter.png|center]]
-==== Inserting molecular models ====
+==== How to insert molecular models in a Moodle page ====
 <!--
 [http://marie.frostburg.edu/101/mod/wiki/view.php?id=787&page=Index Moodle FAQ at  Frostburg State University] explains briefly
@@ Line 55: / Line 55: @@
 #** <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 initial display is the interactive structure (<code>?i=0</code>) or it is a cover image, replaced by the interactive object upon user click (<code>?i=1</code>).
+#* You can also specify whether 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> 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.
@@ Line 61: / Line 61: @@
 === The Jmol resource for Moodle ===
-Jmol models can also be added as [https://docs.moodle.org/20/en/Jmol_resource_type resources].
+Jmol models can also be added as ''Moodle resources''<ref>[https://docs.moodle.org/20/en/Jmol_resource_type Jmol resource type]</ref>.
 <!--
@@ Line 74: / Line 74: @@
 === Internationalization ===
-A project to internationalize the Jmol filter for Moodle was started on 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.

@@ Line 11: / Line 11: @@
 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{{#tag:ref|jmol-developers AT lists.sourceforge.net|name="DevList"}} with information that might be added here.
+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.sourceforge.net</ref> with information that might be added here.
 === The Jmol filter for Moodle ===

@@ Line 16: / Line 16: @@
 A third-party '''Jmol filter''' ([https://docs.moodle.org/36/en/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. no Java) . The user can also opt for the '''JSmol_WebGL''' modality.
+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]].
-* [https://edugit.org/nik/moodle-filter_jmol Download] v.6.5 for Moodle 3.8.2
+* [https://edugit.org/nik/moodle-filter_jmol Download] v.6.5 for Moodle 3.6 to 3.8 at least
 * [https://github.com/geoffrowland/moodle-filter_jmol Download] v.6.4 for Moodle 2.x and 3.x
 * [https://github.com/geoffrowland/moodle-filter_jmol/tree/MOODLE_19_STABLE Download] older versions of the the Jmol filter (e.g. for Moodle 1.8 and 1.9)
@@ Line 31: / Line 31: @@
 -->
 * 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).
+: 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?
-: First, make sure that the administrators of your Moodle site have installed the Jmol filter. Then, simply upload a <code>.pdb</code> file to your course, and make a link to it using Moodle's HTML editor.
+# '''Config:''' First, make sure that the administrators of your Moodle site have installed the Jmol filter.
-: The link must have <code>title="Jmol"</code> for it to work properly.
+# '''Upload files:''' Then, simply upload  to your course a molecular structure file and make a link to it using Moodle's HTML editor.
-: 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.
+::  Formats of molecular structure that are recognized as such, based on the file extension (variable <code>$jmolfiletypes</code> in the filter source code):
- <a href="path/aspartic.pdb">Aspartic acid</a>
+::{| class="wikitable"
-:The default size of the display is 350 pixels. You can set the size of the display to ''n'' pixels by appending <code>?s=n</code> to the URL. For example:
+|-
   <a href="path/aspartic.pdb?s=200">Aspartic acid</a>
-:You can turn the default controls off by appending <code>?c=0</code> to 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 <code>?c=0</code> to the URL. If you combine this with the sizing option, separate the parameters with an ampersand (&).
   <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 <code>JMOLSCRIPT{}</code> after the link. The script goes between the braces.
+#* For even greater control, pass a Jmol script to the view by typing <code>JMOLSCRIPT{}</code> 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="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;}