I too haven't got JMol to work in the NB, although it works fine as
the standalone application when run from the commandline. I don't see
how the site you mentioned would help. Installing JAVA was no problem
and it works just fine, including JMol applets on the jmol.sourceforge
site. This is most likely a problem of SAGE.

I've no ideas how to tackle it. Everything appears to be returned
correctly, from what I can tell, meaning that SAGE provides a JMol
file which says

set defaultdirectory "sage0-size500-306189399.jmol.zip"
script SCRIPT

and the according zip-file has the required contents. However, the
console gives out an error saying

FileManager opening 
http://localhost:8000/home/admin/0/cells/1/sage0-size500.jmol?1276349004
script compiler ERROR: command expected
----line 1 command 1 of /home/admin/0/cells/1/sage0-size500.jmol?
1276349004:
          >>>> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"> <<<<
script ERROR: script compiler ERROR: command expected
----line 1 command 1 of /home/admin/0/cells/1/sage0-size500.jmol?
1276349004:
          >>>> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"> <<<<
eval ERROR:
----line 1 command 1:
         script >> "/home/admin/0/cells/1/sage0-size500.jmol?
1276349004" <<

Any further ideas?

On May 23, 11:39 pm, Bruce Cohen <math.co...@gmail.com> wrote:
> I found this 
> page:http://sites.google.com/site/easylinuxtipsproject/java#TOC-Install-JR...
> to be quite useful.  jmolnow works on all my machines (running Ubuntu
> 10.04)
>
> -Bruce
>
> On May 12, 9:07 pm, Bruce Cohen <math.co...@gmail.com> wrote:
>
>
>
> > I have just triedjmolon two machines running 32 bitUbuntu10.04.
> > At the command line
>
> > var('x y')
> > plot3d(x^2+y^2, (x,-2,2), (y,-2,2))
>
> > works on both machines.
>
> > The same commands in the notebook work fine on the machine with the
> > fresh 10.04 install, but do not work on the one which
> > was upgraded from 9.10.
>
> > On the fresh install, I show this with a url of "about:plugins"
>
> >Java(TM) Plug-in 1.6.0_20
>
> >    File: libnpjp2.so
> >    Version:
> >    The next generationJavaplug-in for Mozilla browsers.
>
> > -Bruce
>
> > On May 12, 5:05 am, Pablo Angulo <pablo.ang...@uam.es> wrote:
>
> > > My experience before 10.04 was that openjdk worked from the command
> > > line, but not in the notebook. This appeared to be the case.
> > > After reading this thread, I tried to drop my .mozilla folder,  which I
> > > have carried for years and now applets do work. More concretely, I
> > > renamed .mozilla into .mozilla-no, and got a freash browser.
> > > I've tried to find the particular file within .mozilla that causes the
> > > trouble, as I want to keep the bookmarks and history, unsuccessfully.
>
> > --
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>
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