sorry for the long mail, I am trying to describe all related details:

it happened yesterday when I followed the link that you posted to your site
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?topic=71

However I can;t seem to reproduce this today.  (it does not happen
every time) From one of my non-public servers which has a pretty
recent (weeks old) version of Jmol.js I just could reproduce this (and
it is the same message as I got from chemapps.stolaf yesterday)

Your web browser is not fully compatible with Jmol
browser: mozilla   version: 5   os: mac   isBrowserCompliant: false
isJavaCompliant: true
mozilla/5.0 (macintosh; intel mac os x 10.6; rv:2.0.1) gecko/20100101
firefox/4.0.1

===

The browser check at http://jmol.sourceforge.net/browsercheck/ gives
a yellow rectangle.

the text is
...

Netscape/Mozilla/FireFox on Macintosh do not have access to the latest
Java release and therefore do not support LiveConnect communications
between JavaScript and Java applets.

The Jmol applet itself will function properly. However, web pages
constructed with HTML controls such as buttons, checkboxes, and links
will not function properly because the controls cannot send the script
commands to the Jmol applet.

...

Operating System        MacOS
Web browser family      mozilla
Browser family version  5
Specific browser
[ navigator.userAgent ]         Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6;
rv:2.0.1) Gecko/20100101 Firefox/4.0.1
Uses the DOM
[ has getElementById() ]        true
Can use Java
[ navigator.javaEnabled() ]     true

code produced by Jmol.js:

<object name='jmolApplet0' id='jmolApplet0'
 width='200' height='200'
 type='application/x-java-applet'
>
  <param name='syncId' value='561441925451007' />
  <param name='progressbar' value='true' />
  <param name='progresscolor' value='blue' />
  <param name='boxbgcolor' value='black' />
  <param name='boxfgcolor' value='white' />
  <param name='boxmessage' value='Downloading JmolApplet ...' />
  <param name='archive' value='JmolApplet0.jar' />
  <param name='mayscript' value='true' />
  <param name='codebase' value='.' />
  <param name='code' value='JmolApplet' />
  <param name='java_arguments' value='-Xmx512m' />
  <param name='script' value='select *' />
<p style='background-color:yellow; color:black;
width:200px;height:200px;text-align:center;vertical-align:middle;'>
You do not have Java applets enabled in your web browser, or your
browser is blocking this applet.<br />
Check the warning message from your browser and/or enable Java applets in<br />
your web browser preferences, or install the Java Runtime Environment
from <a href='http://www.java.com'>www.java.com</a><br /></p></object>

===

My system info is:

OSX 10.6.7
Firefox 4.0.1
plugin JRE version 1.6.0_24-b07-334-10M3326

firefox plugins installed:
web developer, firebug

Andreas

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