Anthony

I really cannot make any logical explanation for the things you are 
seeing. Fortunately, with your downloadable zip I can test; that was 
the best choice, thanks.
I am a Win man so I can test. I do not regularly try IE since it's 
not my favourite and also not the best choice for JSmol with large 
molecules. This is IE11.0.9600, Win8.1, user belongs to admin group

Testing your files, locally:

== test2.htm ==
NCI seems not to deliver the models right now, but PubChem works fine 
in both Firefox and IE

== AntTest.htm ==
loads (surprisingly fast) in IE, both models display

== AntTestPartial_00.htm ==
nothing but several dots in the page

== AntTestPartial_01.htm ==
loads OK in IE

== AntTestPartial_02.htm ==
loads OK in IE

== Antest_old.htm ==
no JSmol box, narrow white space on the left of the texts

== http://chemapps.stolaf.edu/jmol/jsmol/test2.htm  ==
runs OK in Firefox;
in IE I get several alerts but they are related to problems with 
language localization, then at the end the model loads

oh, WAIT!!!!!....  What is your version of IE?  I seem to recall a 
case where a certain old version of IE made JSmol to automatically 
switch to Java -- that would explain your Java errors. I think that 
happened with old IE versions for which there is no support for HTML5 
canvas, so Java is the only choice and the inner code in JSmol 
activates that.
On your frist screenshots there is also the issue of the yellow bar 
at the top of the IE window asking for permission - whatever they say 
("Activex"), you MUST accept and give permission. That explains the 
white boxes.

>From your secreenshots I cannot make what is the IE version (9 is the 
bare minimum if I remember correctly, 10 is much better)

BTW, if you are forced to IE (old or new) and the computers do have 
Java configured, you could be better letting Jmol-Java step in. The 
Java files take less space than the j2s ones and the page code is 
mostly the same


·
 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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