David, works fine for me:
<html>
<head>
<script src="Jmol.js" type="text/javascript"></script>
</head>
<body>
<script type="text/javascript">
jmolInitialize(".")
jmolApplet(300, 'set hoverCallback "alert"; load butane.pdb; ')
</script>
</body>
</html>
Make sure you don't have a quotes conflict
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