Scripting JmolApplet Without Using Jmol.js

Please, note that the methods in this page are not recommended, since they do not use the Jmol.js library. They are kept here for reference, particularly for experienced programmers.

A description of the Jmol implementation of the scripting language is available at Interactive Online Scripting Documentation page.

For small scripts the transition from Chime to Jmol should be straightforward. With larger, more complicated Chime web applications you may have challenges because the button/event mechanism is different. It is strongly recommended that you use the functionality built into Jmol.js, a library written in JavaScript which is included in the standard downloadable Jmol package.

Simple scripts which are executed at applet load time can be executed using the "script" parameter as part of your applet definition in HTML. These scripts will execute on browser platforms which do not support JavaScript or the LiveConnect interface between JavaScript and Java applets. If you choose to use this method, see the examples below.

To develop more flexible web applications using the Jmol applet, you must write JavaScript code which passes text strings using the "script" method of the applet, but you don't need to write the code since it is all easily implemented by using the functions in Jmol.js library.

For additional examples and documentation on Jmol applet scripting see the documentation page.

The following examples are kept for reference by experienced programmers. Please, note that they use the applet tag, with is deprecated since HTML 4 and may become nonfunctional in modern browsers when HTML 5 becomes the default. The recommended altenative is to use the object tag instead, but this is tricky to implement because it requires different code for each browser. Therefore, it is strongly recommended that you make your pages with JmolApplets using the Jmol.js library provided with Jmol distributions, since that takes care of inserting the proper code.

Eye Candy Without JavaScript

This example demonstrates how scripting can be used without JavaScript. Browsers that do not support LiveConnect communication between JavaScript and Java applets will still run this type of script.

<applet name="flash" code="JmolApplet" archive="JmolApplet.jar" codebase="../jmol" width="300" height="100" align="left" mayscript="true"> <param name="bgcolor" value="teal"> <param name="progressbar" value="true"> <param name="script" value=" load jmol.mol; set perspectiveModel 10; set zoomLarge off; select all; cpk off; wireframe 10; color yellow; move 0 0 0 400 0 0 0 0 2; cpk 10; wireframe 5; delay 0.1; cpk 30; wireframe 15; delay 0.1; cpk 50; wireframe 30; delay 0.1; cpk 70; wireframe 50; delay 0.1; select atomno=1, atomno=9; color blue; delay 0.1; select atomno=2, atomno=10; color red; delay 0.1; select atomno=3, atomno=11; color green; delay 0.1; select atomno=4, atomno=12; color orange; delay 0.1; select atomno=5, atomno=13; color pink; delay 0.1; select atomno=6, atomno=14; color brown; delay 0.1; select atomno=7, atomno=15; color purple; delay 0.1; select atomno=8, atomno=16; color cyan; delay 0.1; move 0 0 0 -400 0 0 0 0 1; move 0 0 360 50 0 0 0 0 1; move 0 360 0 350 0 0 0 0 1; loop 5; "> </applet>

Basic Scripting

This example shows some of the scripting available.

<applet name="jmol" code="JmolApplet" archive="JmolApplet.jar"
        codebase="../jmol"
        width="200" height="200" mayscript="true">
  <param name="progressbar" value="true"/>
  <param name="load" value="caffeine.xyz"/>
</applet>
<br/>
<a href="javascript:document.jmol.script('wireframe on; spacefill off;');">
wireframe</a>
<a href="javascript:document.jmol.script('wireframe off; spacefill on;');">
spacefill</a>
<a href="javascript:document.jmol.script('wireframe 0.2; spacefill 25%;');">
ball & stick</a>
<br/>
<a href="javascript:document.jmol.script('load aspirina.mol');">
aspirina.mol</a>
<a href="javascript:document.jmol.script('load bulk_si.in');">
bulk_si.in</a>
<a href="javascript:document.jmol.script('load caffeine.xyz');">
caffeine.xyz</a>
<a href="javascript:document.jmol.script('load dna.xyz');">
dna.xyz</a>
<a href="javascript:document.jmol.script('load estron.cml');">
estron.cml</a>
<br/>
<a href="javascript:document.jmol.script('color background blue ; move 90 180 -45 0 0 0 0 0 5; 
center 1 ; move 0 0 360 100 0 0 0 0 2 ; delay 2 ; reset; color background white')">move</a>
<a href="javascript:document.jmol.script('script move.txt');">
move off of server</a>
<a href="javascript:document.jmol.script('load aspirina.mol')">
load aspirina via script</a>
<a href="javascript:document.jmol.script('script testscript.txt')">
run test script off of server</a>
<br/>
<a href="javascript:document.jmol.script('set perspectiveDepth on')">
perspectiveDepth</a>
<a href="javascript:document.jmol.script('set perspectiveDepth off')">
no perspectiveDepth</a>
<br/>
<a href="javascript:document.jmol.script('color background black')">
black background</a>
<a href="javascript:document.jmol.script('color background grey')">
grey background</a>
<a href="javascript:document.jmol.script('color background [222,222,222]')">
background [222,222,222]</a>
<a href="javascript:document.jmol.script('color background white')">
white background</a>

wireframe spacefill ball & stick
aspirina.mol bulk_si.in caffeine.xyz dna.xyz estron.cml
move move off of server load aspirina via script run test script off of server
perspectiveDepth no perspectiveDepth
black background grey background background [222,222,222] white background

Advanced Scripting

More sophisticated and easier to code methods of interaction are based on JavaScript, and provided by Jmol.js library.

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