Step one is to download the absolutely latest Jmol. If you look at the download page, see under Jmol Prerelease Tests for the cutting edge (currently 11.3.54). There's a new version practically every day. The file you want is called something like jmol-11.3.54-binary.zip. Download and unzip the file into something like D:\Tools\Jmol\jmol-11.3.54.
Next, download the protein structure 1hnn from the PDB and save as something like D:\Proteins\1hnn.pdb.
Now we can create the "Hello World" of Jmol applets, which simply loads and displays the protein structure you have just downloaded. Save the following code as something like D:\Applet\HelloWorld.htm. You should change the paths in the following HTML to correspond to the actual paths on your computer:
var jmolcmds = [
jmolApplet(700, jmolcmds.join("; "));
Open the HTML file with Firefox. The first time you do this, you will be asked whether you trust Jmol to access your hard drive responsibly. You should say yes to this if you wish to proceed. This warning indicates that you are using the signed applet rather than the unsigned applet. Using the signed applet on a live website will probably discourage users, so is best avoided, but it is very useful when running locally on your machine, as the unsigned applet is restricted to opening files in particular directories.
The next post takes Jmol to the next level, uh, level 2.