Jeff,
One good reason to use a separate JS overriding Jmol.js, rather than
modify Jmol.js itself, is that you have an easier route when Jmol.js
is upgraded. The affected function will likely not change, but you
will have to edit teh new Jmol.js again and again to insert your
changes.
I suggest to make a Jmol_xhtml.js file withthe redefined function and
load both files in your pages.
As to the text being interpreted as markup or not, I have no
experience with xhtml, but I read yesterday about the convenience of
using CDATA comments arouns the script tag. Have you tried that?
<script type="text/javascript">
/* <![CDATA[ */
jmolInitialize(".")
jmolApplet(300, 'load "alkaloid.mol"; ')
* ]]> */
</script>
I am setting up my test page at
http://biomodel.uah.es/Jmol/xhtml/
in case anyone is interested
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