> Maybe, but it's not working for me with the current Jmol wiki.
> With Chrome, I get an empty popup about:blank...

That reminds me about something I found previously. Let me see...

>     the HTML code of the main window as Javascript (so it's quite complex). I am looking for a
>     function with simple parameters (mainly, just the URL of the file to be loaded by the Jmol
>     applet) that would then entirely create the popup window.

Well, the HTML code must come from some place :-)
I guess that code could be generated in the Javascript. Does it make any difference to have it there rather than  in the php?