JSmol
JSmol is the name for an alternative to Jmol applet that does not require Java but instead renders the molecular models in a webpage using just JavaScript and HTML5 features. This opens up the use of Jmol not only in PC's, Mac's and Linux's systems without Java installed, but also in tablets and phones (iOS, Android) that do not allow Java or applets. No hardware-based graphics acceleration is used either, and hence it should run in any system that supports HTML5 standards in the web browser. JSmol runs entirely in the client, does not use any server technologies.
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 than Jmol: it is Jmol, just compiled into JavaScript instead of Java (thanks to the Java2Script software).
Current limitations:
- Using local files (i.e. not in a web server) may not be feasible depending on the browser (security policies).
- Opening binary files (e.g Spartan files, gzipped files, PNGJ files): binary files can be read, but not all file types are identified (see below). Also, there are measures to be taken regarding browser compatibility.
- Writing of JPG and PNG data is not supported directly (but see Exporting an image).
- Background images are not supported.
When used together with Jmol JavaScript Object (Jmol-JSO), the same webpage may be authored to run in all devices using in each case a Jmol variety or surrogate that is adjusted to capabilities of each device.
JSmol is still in a development stage, although mostly functional (Feb. 2013). You can see it in action at the test page. Preliminary releases may be obtained at the JSmol Project page and the latest development set of files from St. Olaf.
JavaScript code
The code you must include in your pages is like this:
In the head section:
<script type="text/javascript" src="JSmol.min.js"></script>
<script type="text/javascript">
var Info = {
width: 300,
height: 300,
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php",
use: "HTML5",
j2sPath: "j2s",
console: "myJmol_infodiv"
}
</script>
Please note that although a single JavaScript file is invoked, you must have available in your server the full set contained in the download, since additional components of JSmol will be called as needed by that initial 
JSmol.min.js file. (The total size is around 3 MB, but individual components will be downloaded to the user's machine only as they are needed.)
See Jmol_JavaScript_Object for more details about the Info variable.
And in the <body> section:
<script type="text/javascript">
myJmol = Jmol.getApplet("myJmol", Info);
</script>
Reading binary files
These are currently the extensions that make JSmol read a file as binary: .gz
.jpg
.png
.zip
.jmol
.bin
.smol
.spartan
.mrc
.pse
If you rename any file to include .bin in its name, that will instruct JSmol to read it as a binary file.
In adition, for binary file reading to be compatible with Chrome and MSIE, you will need to have a base64 server-side piece that will convert the binary data to BASE64 format. This is because only Firefox allows clean (reliable) synchronous binary file transfer. The demo pages use a jsmol.php file, which does that and considerably more.
