JSmol Object - Revision history

AngelHerraez: fix missing redirects

2025-08-11T16:52:05Z

fix missing redirects

AngelHerraez: some polishing and updated terminology

2025-08-11T10:54:21Z

some polishing and updated terminology

AngelHerraez: some polishing and updated terminology

2025-08-11T10:47:27Z

some polishing and updated terminology

AngelHerraez: AngelHerraez moved page Jmol Applet to JSmol Object: remove old mentions of Java Applet, reinforcing the JSmol term

2025-08-11T10:15:51Z

AngelHerraez moved page Jmol Applet to JSmol Object: remove old mentions of Java Applet, reinforcing the JSmol term

AngelHerraez: /* Testing different JSmol versions */

2024-11-30T00:54:53Z

‎Testing different JSmol versions

AngelHerraez: /* Forcing the JSmol object to open in a certain language */

2021-08-14T10:29:12Z

‎Forcing the JSmol object to open in a certain language

AngelHerraez: moving aside the legacy information (applet)

2020-02-11T11:56:01Z

moving aside the legacy information (applet)

Show changes

AngelHerraez: /* Jmol object */

2017-03-15T23:42:25Z

‎Jmol object

AngelHerraez: /* Testing different JSmol versions */

2016-06-22T07:15:09Z

‎Testing different JSmol versions

AngelHerraez: update for JSmol - forcing language or Jar version

2016-06-21T22:24:51Z

update for JSmol - forcing language or Jar version

@@ Line 16: / Line 16: @@
 Which are those necessary files? Read subsections below.
-To use the Jmol object within local web pages, e.g. on the hard disk or on CD, see [[Jmol Applet Deployment Local]] for some precautions needed.
+To use the Jmol object within local web pages, e.g. on the hard disk or on CD, see [[JSmol Deployment Local]] for some precautions needed.
 If you distribute your web page files, you should also include the copyright, license and information files: {{File|COPYRIGHT.txt}}, {{File|LICENSE.txt}} and {{File|README.txt}}

@@ Line 78: / Line 78: @@
 :''Warning'': At least in Windows, modern browsers may detect this action as opening a pop-up window, so it's likely that the pop-up blocker will prevent you from seeing the "Open or Save" dialog. Pay attention to messages and options in your browser to allow pop-ups for the current page. (Such messages often appear as yellow bars at the top of the page, warnings in a toolbar, or hints in the status line at the bottom of the browser window.)
-In addition to saving the full model, a '''part of the molecule''' can be extracted and saved into MOL format. This is not so straightforward as the former, and is described in the "interactive scripting documentation" (see [{{Website}} Jmol home page]).
+In addition to saving the full model, a '''part of the molecule''' can be extracted and saved into MOL format. This is not so straightforward as the former, and is described with the <code>write</code> command in the [{{ScriptingDoc}}#writemodel Interactive Scripting Documentation].
-It is also possible to save the '''state of the molecule''' (rendering style, coloring, visibility, orientation, etc.). See [http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#save <code>save state</code>] and [http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#write <code>write state</code>] in the Jmol scripting documentation.
+It is also possible to save the '''state of the molecule''' (rendering style, coloring, visibility, orientation, etc.). See [{{ScriptingDoc}}#save <code>save state</code>] and [{{ScriptingDoc}}#write <code>write state</code>] in the scripting documentation.

@@ Line 1: / Line 1: @@
-''Note: although the title of this page remains the same, there is no longer any implication of Java applets involved in running Jmol''
+''Note: even though some mentions of "Jmol Applet" may remain, there is no longer any implication of Java applets involved in running J(S)mol''
 {{Lang:Jmol Applet}}
@@ Line 5: / Line 5: @@
 {{Running_Jmol_Sections}}
-== Jmol HTML5 Object (JSmol) ==
+<big>JSmol</big> (the Jmol HTML5 Object, also formerly Jmol JavaScript Objcet or Jmol-JSO) allows to embed in web pages a panel with the functionalty of Jmol. Like with the Jmol application, commands can be applied to the model using the [[Scripting]] language. For some demonstration pages see {{Website}}demo/. To see the HTML source use your web browser {{MenuItem|View}} &rarr; {{MenuItem|Page Source}}.
-This allows Jmol to be embedded in web pages. Like with the application, commands can be applied to the model using the [[Scripting]] language. For some demonstration pages see {{Website}}demo/. To see the HTML source use your web browser {{MenuItem|View}} &rarr; {{MenuItem|Page Source}}.
+== Installing JSmol objects ==
 {{Installing_Jmol_Sections}}
-If you only wish to create a web page(s) containing molecular scenes in Jmol, there are easier ways than starting from scratch: see [[#Tools for Authoring Jmol Web Pages]]. If you wish to learn how to create web pages containing Jmol from scratch, read on.
+If you only wish to create web page(s) containing molecular scenes in Jmol, there are easier ways than starting from scratch: see [[#Tools for Authoring Jmol Web Pages]]. If you wish to learn how to create web pages containing Jmol from scratch, read on.
 Download the Jmol package (either <code>.zip</code> or <code>tar.gz</code> format) and extract/uncompress '''only the necessary files''' to the folder of your choice.
@@ Line 19: / Line 17: @@
 To use the Jmol object within local web pages, e.g. on the hard disk or on CD, see [[Jmol Applet Deployment Local]] for some precautions needed.
 If you distribute your web page files, you should also include the copyright, license and information files: {{File|COPYRIGHT.txt}}, {{File|LICENSE.txt}} and {{File|README.txt}}
-=== Inserting Jmol objects into web pages ===
+=== Inserting JSmol objects into web pages ===
-Inclusion of Jmol objects and interaction with them are managed easily using a JavaScript-based solution:
+Inclusion of JSmol objects and interaction with them are managed easily using a JavaScript-based solution:
-==== Jmol JavaScript Object (Jmol-JSO) ====
+==== JSmol ia a Jmol JavaScript Object (Jmol-JSO) ====
-'''Jmol-JSO''' (new in Jmol v.13) provides a clean, efficient way to interact with the Jmol applet from JavaScript and, in addition, allows extension to Java- and applet-challenged platforms such as the iPad, the iPhone, and Android mobile devices, and adds easy access to public databases such as [http://rcsb.org the RCSB PDB database], [http://cactus.nci.nih.gov/ the National Cancer Institute CACTVS server], and [http://pubchem.ncbi.nlm.nih.gov/ PubChem], even when the Jmol Java applet is not available because of a user's platform. Basic high-level scripting for these non-Java alternatives is included. In addition, '''Jmol-JSO''' adds synchronization with the [http://jspecview.sourceforge.net JSpecView applet] and 2D-to-3D model building and interconversion using the [https://peter-ertl.com/jsme/ JSME Molecule Editor]. See more details on [[Jmol JavaScript Object]].
+'''JSmol''' provides a clean, efficient way to interact with Jmol functionality from JavaScript avoiding the legacy need for using Java inside web pages. In addition, '''JSmol''' adds synchronization with the [https://jspecview.sourceforge.net JSpecView applet] (now converted to JavaScript-only version) and 2D-to-3D model building and interconversion using the [https://peter-ertl.com/jsme/ JSME Molecule Editor]. See more details on [[Jmol JavaScript Object]].
 ====  Forcing the JSmol object to open in a certain language ====
@@ Line 52: / Line 48: @@
 ''This may work or not, depending on the page code and on the JSmol versions.''
-== Jmol in Wikis ==
+== JSmol in Wikis ==
-The applet can be embedded in [[wikipedia:HTML|HTML]] (or XHTML) pages (examples are listed on [[Websites Using Jmol]]), but also, with some extra technologies, in Wiki pages (see [[Jmol Processor]]).
+JSmol can be embedded in [[wikipedia:HTML|HTML]] (or XHTML) pages (examples are listed on [[Websites Using Jmol]]), but also, with some extra technologies, in Wiki pages (see [[Jmol Processor]]).
-== Tools for Authoring Jmol Web Pages ==
+== Tools for Authoring JSmol Web Pages ==
-===Jmol.php: easy Jmol insertion into a web page===
+===Jmol.php: easy JSmol insertion into a web page===
-You can insert a Jmol object into a web page with nothing more than a simple <code><script></code> or <code><a></code> tag.
+You can insert a JSmol object into a web page with nothing more than a simple <code><script></code> or <code><a></code> tag.
 You don't have to install any Jmol files in your computer or web server.
 You don't even need a file with the 3D model; it will be automatically obtained from an appropriate web server.
-Note that this way of using Jmol is easily compatible with any environment where you do not control the full source code, like forums, blogs, wikis, content management systems, e-learning environments...
+Note that this way of using JSmol is easily compatible with any environment where you do not control the full source code, like forums, blogs, wikis, content management systems, e-learning environments...
-In fact, you can email the address and the recipient will see the Jmol object by clicking on the received link.
+In fact, you can email the address and the recipient will see the JSmol object by clicking on the received link.
 See [[Jmol_PHP]] for details.
 ===Proteopedia's Scene Authoring Tools===
-The easiest way to create, and share, a web page containing customized molecular scenes in Jmol, is to build the page in [http://proteopedia.org Proteopedia.Org]. Proteopedia's ''Molecular Scene-Authoring Tools'' free you from learning any Jmol commands, HTML, or javascript. You will only need to learn a tiny bit of wikitext markup, for which convenience buttons and help are provided. On the other hand, if you already know some Jmol commands, you may use them in creating your scene (via the Jmol console). Regardless of how your scene is created, it will be saved as a Jmol state script. You may upload atomic coordinate files, or use published PDB files. Proteopedia automatically saves a frozen copy of each PDB file that you use, to protect your scripts from breaking e.g. after remediation of files by the Protein Data Bank. You may created pages that are protected from editing by others.
+The easiest way to create, and share, a web page containing customized molecular scenes in JSmol, is to build the page in [http://proteopedia.org Proteopedia.Org]. Proteopedia's ''Molecular Scene-Authoring Tools'' free you from learning any Jmol commands, HTML, or javascript. You will only need to learn a tiny bit of wikitext markup, for which convenience buttons and help are provided. On the other hand, if you already know some Jmol commands, you may use them in creating your scene (via the JSmol console). Regardless of how your scene is created, it will be saved as a Jmol state script. You may upload atomic coordinate files, or use published PDB files. Proteopedia automatically saves a frozen copy of each PDB file that you use, to protect your scripts from breaking e.g. after remediation of files by the Protein Data Bank. You may also create pages that are protected from editing by others.
 ===Jmol's ''Export to Web''===
-If you are not comfortable writing html/xhtml and javascript code, or would just like to quickly put together some simple pages, then look at the '''export to web function of Jmol'''.  This allows you to export all the necessary files to make simple pages that have a number of live Jmol displays or a single Jmol display that can be changed by clicking buttons.  You select the views you want the user to see by setting them up in Jmol.  You then add any desired text or comments to the .html file created by the export function in your favorite web editor (Some open source suggestions: [http://www.seamonkey-project.org/ SeaMonkey] is simple and works very well, [http://www.kompozer.net/ Kompozer] is more sophisticated and works pretty well, [http://www.w3.org/Amaya/ Amaya] is the most sophisticated but is harder to use). Instructions for using the export function are accessible in the export to web dialog within the Jmol application.  A more detailed tutorial and some older packages are available at [http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Jmol_Web_Page_Maker.shtml Jmol Web Page Maker].
+If you are not comfortable writing html/xhtml and javascript code, or would just like to quickly put together some simple pages, then look at the '''export to web function of Jmol'''.  This allows you to export all the necessary files to make simple pages that have a number of live JSmol displays or a single JSmol display that can be changed by clicking buttons.  You select the views you want the user to see by setting them up in Jmol.  You then add any desired text or comments to the .html file created by the export function in your favorite web editor (Some open source suggestions: [http://www.seamonkey-project.org/ SeaMonkey] is simple and works very well, [http://www.kompozer.net/ Kompozer] is more sophisticated and works pretty well, [http://www.w3.org/Amaya/ Amaya] is the most sophisticated but is harder to use). Instructions for using the export function are accessible in the export to web dialog within the Jmol application.  A more detailed tutorial and some older packages are available at [http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Jmol_Web_Page_Maker.shtml Jmol Web Page Maker].
 <!--[[User:Gutow|Gutow]] 21:48, 25 July 2008 (CEST)-->
-== Saving Files from the Jmol Object ==
+== Saving Files from the JSmol Object ==
 Although this isn't obvious, the molecule that is being shown in JSmol can be saved to local disk unless the model was loaded inline, in which case this technique fails. To do so:
-# Open the applet's menu (right-click, Ctrl+click, or click on bottom-right "Jmol" logo).
+# Open JSmol context menu / pop-up menu (right-click, Ctrl+click, or click on bottom-right "JSmol" logo).
-# Click on the last entry (<code>About...</code>).
+# Click on the first entry (<code>File...</code>), then <code>Save...</code> and <code>Save a copy of...</code>.
 # Depending on your browser's configuration, the file will be opened in the associated program ("helper application") or you will get an "Open or Save" dialog; choose Save and location in your disk.

@@ Line 45: / Line 45: @@
 On the URL line of the browser, add the following:
-''(Pending -- this needs verification)''
+<code>?_J2S=</code> followed by the url of the {{folder|j2s}} folder your intend to use.
-<!-- need to check if this works
+Note: uppercase is needed for the part before =
 If there is already a <code>?</code> in the URL, then use <code>&</code> for your addition, to preserve the logic of a url.
--->
 == Jmol in Wikis ==

@@ Line 35: / Line 35: @@
 # The language in JSmol can be switched anytime, from the pop-up  menu, "Language" item near the bottom.
-# Or, using the scripting language: <code> language = "de" </code> (you must use the keyword "language" and the two-letter language code: ca, cs, de, en, es, et, fr, nl, pt, tr, etc.).
+# Or, using the scripting language: <code> language = "de" </code> (you must use the keyword "language" and the two-letter language code: ca, cs, de, en, es, et, fr, nl, pt, tr, etc.). In a few cases, the language code has 2+2 letters: en_GB, en_US, pt_BR, zh_CN, zh_TW
 === Testing different JSmol versions ===

← Older revision	Revision as of 10:15, 11 August 2025
(No difference)

@@ Line 6: / Line 6: @@
 === Jmol Applet ===
 [[wikipedia:Java_applet|Java applet]] version of Jmol which allows Jmol to be embedded in web pages (given that viewers have a Java plugin installed). Like with the application, commands can be applied to the model using the [[Scripting]] language. For some demonstration pages see {{Website}}demo/. To see the HTML source use your web browser {{MenuItem|View}} &rarr; {{MenuItem|Page Source}}.
 === Jmol HTML5 Object (JSmol) ===

← Older revision		Revision as of 07:15, 22 June 2016
Line 108:		Line 108:

	There will be a couple of warnings that you will have to accept, due to the potential security risk of replacing an applet with another coming from a totaly unrelated server. There may also be Java security issues still preventing the applet from loading files, unless you specify the signed applet.		There will be a couple of warnings that you will have to accept, due to the potential security risk of replacing an applet with another coming from a totaly unrelated server. There may also be Java security issues still preventing the applet from loading files, unless you specify the signed applet.
		+
		+	For example:
		+	<nowiki>http://proteopedia.org/w/Acetyl-CoA_carboxylase?</nowiki><font color=red><nowiki>_USE=JAVA&JAR=http://chemapps.stolaf.edu/jmol/jsmol/java/JmolAppletSigned0.jar</nowiki></font>
		+	lets you use Bob's latest version of Jmol for that Proteopedia page.
		+	[http://proteopedia.org/w/Acetyl-CoA_carboxylase?_USE=JAVA&_JAR=http://chemapps.stolaf.edu/jmol/jsmol/java/JmolAppletSigned0.jar Try it].

	<!-- not working now --need to check:		<!-- not working now --need to check: