Thank you so much for the clarification. You were spot on.

I now fully understand the difference. I am happy with JSmol as I do not want to rely on Java.


On Tue, Sep 24, 2013 at 11:43 AM, Angel Herráez <> wrote:
At the risk of being repetitive, let's set this clear:

Old and new Jmol needs Java, both for the application (stand-alone
program in your computer) and for the applet inside webpages (using
the Java plugín which is installed/added to your browser when you
install Java in the computer).

Current policies of both Java and the browsers make more difficult to
run Java applets, needing permissions, confirmation dialogs and so.
Still, they runs nicekly once you are confident to give the
permissions (except for pages with applets in local disk, which are
nearly impossible to run now).

Java runs in the client machine. The applet gets downloaded as part
of the page.

New JSmol (only used as objects inside webpages, no application here)
does not use Java. It runs JavaScript + HTML5 code, in the browser.
All modern browsers can run it (that means Internet Explorer mst be
version 10, maybe 9 too --can't remember now; no problems with
Safari, Chrome, Firefox, Opera?).
There is NO Java requirement at all. This caters for those who don't
want or are not allowed to install Java in their computer, and for
devices that do not support Java --like iOS and Android

Javascript runs in the client machine too.

So in any case the server only delivers the pages. There are a couple
of exceptions (loading binary files, loading files from external
databases) but we can omit that for this general description.

What Jmol2.js does is convert your existing page with JmolApplets
based on Jmol.js to the new Jmol-JSO format (that's Jmol JavaScript
Object) --withuout you ever changing a bit in the page code**.
Jmol-JSO may be set to use Java Jmol applets or use HTML4 JSmol. You
need to configure that in your copy of Jmol2.js.

(( ** Well, you do need to change 2 lines in your page headers. See
the Wiki. ))

Please re-read the documentation we have. I know it is not extensive,
but I think it does explain most of these things.

And you are always welcome to contribute in the Wiki contents.

Good luck with your J(S)mol prjects!

October Webinars: Code for Performance
Free Intel webinars can help you accelerate application performance.
Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
the latest Intel processors and coprocessors. See abstracts and register >
Jmol-users mailing list