Well, Michael, your snip of html code is working for me.
I see a full-window JSmol!  -- background is white but the logo is 
there.

> <html> <head> <script type="text/javascript" 
src="Jmol.js"></script>
> <title>JmolinVB</title> </head>
> <body> <script type="text/javascript">
> jmolApplet(0.99), jmolBr(), jmolCommandInput()
> </script> </body> </html>

So maybe you are lacking some of the JSmol files and folders. 
Specifically, the "j2s" folder is used by JSmol/html5  while the 
"java" folder is used by Jmol/Java. Those should be present alongside 
the combined Jmol.js


> that does raise another question.  You can apparently use a header or 
> REMARK after the "model", but your header should not simply be a 
> number.  Apparently Angel knew that the number should be dropped when 
> using ATOM.

Because the single number is not valid PDB syntax. You could have 
"REMARK   2 " or "REMARK 1734" without any problem.


·
 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28871 Alcalá de Henares  (Madrid), Spain


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