Difference between revisions of "Jmol Applet"

From Jmol
Jump to navigation Jump to search
(adding snapshot)
(moving aside the legacy information (applet))
 
(37 intermediate revisions by 7 users not shown)
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''
 +
 
{{Lang:Jmol Applet}}
 
{{Lang:Jmol Applet}}
  
 
{{Running_Jmol_Sections}}
 
{{Running_Jmol_Sections}}
== 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, [[Scripting]] is available. For some demonstration pages see http://www.jmol.org/demo/. To see the HTML source use your web browser {{MenuItem|View}} → {{MenuItem|Page Source}}.
+
== Jmol HTML5 Object (JSmol) ==
 +
 
 +
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}} → {{MenuItem|Page Source}}.
 +
Starting with version 13.1, Jmol may also be inserted into web pages using the non-Java alternative, called JSmol. This allows to use an HTML5 object that only requires JavaScript and has the same set of features as Jmol applet. See [[Jmol JavaScript Object]] for more details.
  
== Installing Jmol Applet ==
+
== Installing Jmol objects ==
 
{{Installing_Jmol_Sections}}
 
{{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.
 +
 
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.
 
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.
  
Which are those necessary files? For basic use, these:
+
Which are those necessary files? Read subsections below.
* {{File|Jmol.js}}, this contains a set of scripting commands that are helpful for interacting with Jmol via a web page (functions for buttons, checkboxes, etc. to interact with the applet). For an overview of functions see the [http://jmol.sourceforge.net/jslibrary/ online documentation] or, for the most up-to-date info, just browse the Jmol.js sourcefile.
 
* All files whose name starts with {{File|JmolApplet0}} and ends in {{File|.jar}}
 
* If you will 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}}
 
  
To use JmolApplet 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 [[Jmol Applet Deployment Local]] for some precautions needed.
  
 
For some specific needs, you must use other files; read the sections below about the signed applet.
 
For some specific needs, you must use other files; read the sections below about the signed applet.
  
If the applet does not load, see also [[Solving Java Problems]].
+
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 ===
 +
Inclusion of Jmol objects and interaction with them are managed easily using a JavaScript-based solution:
  
=== Giving JmolApplet more memory to work with ===
+
==== Jmol JavaScript Object (Jmol-JSO) ====
Memory available to Jmol is determined by Java. You can check the current memory allocation by opening the pop-up menu in the applet, and the last submenu "About Jmol".
+
'''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]].
  
Less or more memory can be allocated by using this parameter:
+
==== Forcing the JSmol object to open in a certain language ====
  -Xmx###M
+
The JSmol object includes [[Internationalisation/Current_Status|several languages]] (technically called localizations) for the user interface (pop-up menu). JSmol will open by default with the interface using the language of your operating system
where the ### must be substituted by a number in megabytes (hence the "M" after it). However, the amount of memory that can be allocated is limited by your existing RAM. For example, on a system with 512 MB RAM, a maximum of 256 MB is allowed for Java.
+
([http://java.sun.com/j2se/corejava/intl/reference/faqs/index.html#set-default-locale ref.]). However, if you need to change this:
 
 
Examples:
 
* -Xmx512M  will give 512 Mb maximum memory available.
 
* -Xmx1024M    will give 1024 Mb maximum memory available.
 
 
 
The place to set this parameter is:
 
 
 
:'''Windows''':
 
 
 
::Control Panel > Java icon (opens the [[Solving_Java_Problems#Java_Control_Panel|Java Control Panel]]) > "Java" tab > "Applet run-time configuration" > "Show" button > on row "JRE" (latest version if there are several), click on the textbox under "Parameters" and type: -Xmx###M
 
 
 
:'''Macintosh''':
 
 
 
::Under /Applications/Utilities/Java/J2SE 5.0/Java Preferences, look for the place to put the -Xmx###M
 
::Or look in the [[Solving_Java_Problems#Java_Control_Panel|Java Control Panel]].
 
  
Note that this is a local setting, so it will only affect that computer. You cannot expect that visitors of your web pages will have the same Java memory configuration as you, so be careful when using this feature.
+
# 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.).
  
Technical details:
+
=== Testing different JSmol versions ===
* -Xmx sets the maximum memory heap size.
+
''(This is an advanced feature)''
* -Xms sets the minimum memory heap size.
 
  
See also [[Jmol_Application#Giving_Jmol_more_memory_to_work_with|the procedure for the application]].
+
You can force the use of a certain version of JSmol object in any web page (even if that page is not yours), as long as the page was written using the standard, recommended code for inserting JSmol objects. The way to do so is:
  
===  Forcing JmolApplet to open in a certain language ===
+
On the URL line of the browser, add the following:
JmolApplet [[Internationalisation/Current_Status|includes several languages]] (technically called localizations) for the user interface (pop-up menu).
 
JmolApplet will open by default with the interface using the language
 
of your operating system
 
([http://java.sun.com/j2se/corejava/intl/reference/faqs/index.html#set-default-locale ref.]). However, if you need to change this:
 
  
# Starting Jmol 11.1.30, the language in the applet can be switched anytime, from the pop-up  menu, "Language" item near the bottom.
+
''(Pending -- this needs verification)''
# 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)
+
<!-- need to check if this works
# ''This is an old method, only needed for versions below 11.1.30:'' If you want to force a certain language,
+
<code>?_USE=HTML5&J2S=</code> followed by the url of the {{folder|j2s}} folder your intend to use.
<blockquote>
 
  <blockquote>
 
'''On Windows''':
 
Open Windows Control Panel > Java icon (opens Java Control Panel) > Java tab > Applet run-time configuration > Show button >
 
on row "JRE", click on the textbox under "Parameters" and type:
 
<pre>
 
  java -Duser.language=es    # forces Spanish (Español)
 
  java -Duser.language=de    # forces German (Deutsch)
 
  java -Duser.language=en    # forces English
 
  etc.
 
</pre>
 
  </blockquote>
 
  <blockquote>
 
'''On Macintosh''':
 
Open the Java Control Panel at /Applications/Utilities/Java/J2SE 5.0/Java Preferences and set the parameter as above.
 
  </blockquote>
 
</blockquote>
 
  
See also [[Jmol_Application#Forcing_Jmol_to_open_in_a_certain_language|the procedure for the application]].
+
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 ==
 
== Jmol in Wikis ==
Line 85: Line 55:
 
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]]).
 
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]]).
  
== Unsigned vs. Signed Applet & Data Access ==
+
== Tools for Authoring Jmol Web Pages ==
 +
===Jmol.php: easy Jmol 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 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...
 +
In fact, you can email the address and the recipient will see the Jmol object by clicking on the received link.
  
[[File:Java_Warning_Signed.gif|right|300px]]
+
See [[Jmol_PHP]] for details.
The '''signed''' applet can load a molecular model from any http or ftp URL. However, the user will be asked to trust the signed applet (figure at right). This could be problematic since the publishing authority (jmol.org) "cannot be verified", and the security certificate was issued by a group that is "not trusted" (jmol.org). This is because it would be costly and cumbersome for each version of the applet to be signed by a trusted (commercial) authority.
 
  
The '''unsigned''' applet displays the molecule without asking the user to trust it. However, it is limited (for security reasons) to loading molecular models from the same http domain (server) that downloads the applet itself. [http://firstglance.jmol.org/ FirstGlance in Jmol] uses the unsigned applet by default, but the signed applet will be used when that "Advanced Option" is checked. Thus you can easily see both applets in action. Methods for accessing data files from arbitrary servers are described in some detail at [http://bioinformatics.org/firstglance/fgij/datameth.htm PDB Data File Access Methods].
+
===Proteopedia's Scene Authoring Tools===
<br>
+
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.
If you are ''not'' running the applet from any server, i.e., you are using a web page residing in a '''local disk''', further security restrictions are applied by Java: molecular models can only be located in the same folder/directory as the applet files or below it; read [[Jmol Applet Deployment Local]].
 
  
== Tools for Authoring Jmol Web Pages ==
+
===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 look at the export to web function of Jmol (available in version 11.4 and above).  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].--[[User:Gutow|Gutow]] 21:48, 25 July 2008 (CEST)
+
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].
 +
<!--[[User:Gutow|Gutow]] 21:48, 25 July 2008 (CEST)-->
  
== Saving Files from the Applet ==
+
== Saving Files from the Jmol Object ==
Although this isn't obvious, the molecule that is being shown in the applet can be saved to local disk. To do so:
+
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 applet's menu (right-click, Ctrl+click, or click on bottom-right "Jmol" logo).
+
# Open the applet's menu (right-click, Ctrl+click, or click on bottom-right "Jmol" logo).
# Click on topmost entry (name of molecule).
+
# Click on the last entry (<code>About...</code>).
# On the submenu that appears, click on bottommost entry (name of file).
+
# On the submenu that appears, the first entry is the name of the first model loaded. If it says "string" then the model was loaded inline and continuing will result in a "404" resource not found error. If the entry is a file name, then you can continue.  If more than one file has been loaded, there will be a line for each on this submenu. Click on the one that you want to open or save.  This will bring up another layer of menu options
 +
# Click on the last entry (<code>View</code> + name of file)
 
# 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.
 
# 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.
  
 
:''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.)
 
:''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.)
  
:''Note for Chime users'': If you have MDL Chime installed, the molecule will be opened in a browser window using Chime. You just have to use Chime's menu (File > Save molecule as) to save the file to disk.
+
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]).
 
 
More user-friendly ways or saving files from JmolApplet are being considered by the developers.
 
 
 
In Jmol v.11, 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 [http://jmol.org/ Jmol home page]).
 
  
The ability to save the state of the molecule (rendering style, coloring, visibility, orientation, etc.) is under development, and already partially implemented in Jmol 11.0. 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. This will give similar functionality to what can be done in Chime or Rasmol, although due to Java security restrictions, saving to a file is not available for JmolApplet.
+
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.

Latest revision as of 11:56, 11 February 2020

Note: although the title of this page remains the same, there is no longer any implication of Java applets involved in running Jmol


Geographylogo.png

Reference: English – Other: 日本語 ·


Running Jmol / JSmol

Jmol HTML5 Object (JSmol)

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 http://jmol.sourceforge.net/demo/. To see the HTML source use your web browser ViewPage Source. Starting with version 13.1, Jmol may also be inserted into web pages using the non-Java alternative, called JSmol. This allows to use an HTML5 object that only requires JavaScript and has the same set of features as Jmol applet. See Jmol JavaScript Object for more details.

Installing Jmol objects

Installing Jmol / JSmol

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.

Download the Jmol package (either .zip or tar.gz format) and extract/uncompress only the necessary files to the folder of your choice.

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.

For some specific needs, you must use other files; read the sections below about the signed applet.

If you distribute your web page files, you should also include the copyright, license and information files: File icon.gifCOPYRIGHT.txt, File icon.gifLICENSE.txt and File icon.gifREADME.txt

Inserting Jmol objects into web pages

Inclusion of Jmol objects and interaction with them are managed easily using a JavaScript-based solution:

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 the RCSB PDB database, the National Cancer Institute CACTVS server, and 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 JSpecView applet and 2D-to-3D model building and interconversion using the JSME Molecule Editor. See more details on Jmol JavaScript Object.

Forcing the JSmol object to open in a certain language

The JSmol object includes several languages (technically called localizations) for the user interface (pop-up menu). JSmol will open by default with the interface using the language of your operating system (ref.). However, if you need to change this:

  1. The language in JSmol can be switched anytime, from the pop-up menu, "Language" item near the bottom.
  2. Or, using the scripting language: language = "de" (you must use the keyword "language" and the two-letter language code: ca, cs, de, en, es, et, fr, nl, pt, tr, etc.).

Testing different JSmol versions

(This is an advanced feature)

You can force the use of a certain version of JSmol object in any web page (even if that page is not yours), as long as the page was written using the standard, recommended code for inserting JSmol objects. The way to do so is:

On the URL line of the browser, add the following:

(Pending -- this needs verification)

Jmol in Wikis

The applet can be embedded in 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

Jmol.php: easy Jmol insertion into a web page

You can insert a Jmol object into a web page with nothing more than a simple <script> or <a> 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... In fact, you can email the address and the recipient will see the Jmol 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 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.

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: SeaMonkey is simple and works very well, Kompozer is more sophisticated and works pretty well, 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 Jmol Web Page Maker.

Saving Files from the Jmol 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:

  1. Open the applet's menu (right-click, Ctrl+click, or click on bottom-right "Jmol" logo).
  2. Click on the last entry (About...).
  3. On the submenu that appears, the first entry is the name of the first model loaded. If it says "string" then the model was loaded inline and continuing will result in a "404" resource not found error. If the entry is a file name, then you can continue. If more than one file has been loaded, there will be a line for each on this submenu. Click on the one that you want to open or save. This will bring up another layer of menu options
  4. Click on the last entry (View + name of file)
  5. 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.
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 Jmol home page).

It is also possible to save the state of the molecule (rendering style, coloring, visibility, orientation, etc.). See save state and write state in the Jmol scripting documentation.