I have to pardon my self, I wasn't looking carefully enough at Jmol.js and JmolCore.js, JmolApplet.js and JmolApi.js, and it looks that I kinda misjudged the applet initialiation process. Sorry about that :) As you alerady mentioned in your example "Jmol.setDocument(0);". So there seems to be no problems with that, my bad. :/
A good challenge for you would be to rewrite http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm using your alternative approach. Allow no JavaScript within the <body> (right?). Make sure it still works properly on iPad, iPhones, and Android tablets. The challenge would be to make it as simple as what you see there.

I say challange accepted, just give me some few weeks, as I have to dig deeper into ChemDoodle, JME and JSpecView APIs. My main intention was to create an alternative for Jmol.js only (and kinda stripped down version, as I said it was intended only for core build-up and communication), but now I see the possibilities in those new sample pages, where you can turn Jmol into JME seamlessly, and that kinda intrigues me. I'd be glad to create a jQuery version for JME too.
jmolButton is simply a higher level interface that allows page developers to quickly introduce functionality so that they don't have to mess with  "IE way" and "others". We really do not want page developers messing with that. Three years from now there will be another way for another random browser. This is asking to have broken pages that require difficult maintenance. But I think you know that and must mean that these would be within some other API.
The "IE way" and "others" example was intended to show low level JavaScript approach, that I saw proper. If I manage to somehow convince you to start using jQuery, all that pain would go away, because jQuery smoothly wraps all these different browser event binding problems away from us.
Well, actually, that won't work. Jmol scripts can be quite complicated, and some have enough quoting in them that they don't lend themselves to being expressed as attributes. jmolButton and other controls allow for a higher level of use that hides all that complexity. Are you suggesting the page developer writes that tag themselves? If so, then I think you are just going back to an earlier stage in our process (about  8 years ago) and not appreciating the advantage of a JavaScript library such as Jmol.js. If you mean that some API would write this tag, OK, but I don't see the advantage then of that over jmolButton.
If we return to my point of separating JS from HTML, I say don't worry about complicated scripts. HTML was intended (by Sir Tim Berners Lee) as a markup for data.

So I say there is no problems with writing simple HTML with data attributes containing some hard core scripts. Maybe, if you have some really nasty examples, that have strict indenting and line breaks, that you could show me and I could test them, then, please, show me them.

As for quotes - always escape them. If the site is running with some kinda CMS, that can be done automatically in WYSIWYG, if the site is prepared with some authoring tool, like, for example, Dreamweaver, then it will also do it for you.

I should note that Jmol.js and JmolApi.js both  allow simple

<div id="xxxx"></div>

within the body and all Jmol calls in the head to populate those. Most developers I've talked with just don't find that any easier. I actually like it, because it nicely separates the page formatting (in the body) from the dynamics (in the head). But still, I rarely do it unless I really have to. Jmol calls within the body are really just implementing static code anyway, so one could argue that's where they should be. But that's probably old school...
Yes, I was not paying enough attention to whole inner workings of Jmol.js and JmolApplet.js, maybe beause I was more looking at example code that used inline scripting, and that kinda made me a wee bit angry :)

We could probably do a lot more with jQuery, but since it's only needed for the AJAX, we haven't felt it necessary to do more with it.
var jmol; // This is the Jmol object on which we are working on
function myclick_listener_function(e){
  e.preventDefault(); // If it's a link tag for example, we kill it's default behaviour
  var scriptStr = $(this).data('script'); // We could store all the scripting in HTML code in HTML5 data attributes
  Jmol.script(jmol, scriptStr); // This is where we call Jmol OOP framework and send some commands to our Jmol applet
    $('#mybutton').bind('click', myclick_listener_function);

And this is easier than

Jmol.jmolButton(jmol, "myscript", "mytag")

? What makes that particularly appealing to you?
Jmol.jmolButton() returns HTML instead of HTML already being prepared in the body, that's it. Basically, the main concern I see is that JavaScript is doing stuff it could be freed of - like generating HTML where it's not really necessary. JavaScript is great for adding action to static HTML, but why should one use it create HTML? Let's say we have my one and only example:

<p><a href="some_molecule.pdb" class="jmol-load">DNA</a></p>

If Jmol didn't load properly or JavaScript has been disabled, this allows user to download a PDB file and open it up in whatever software he likes. If JavaScript is disabled Jmol.jmolButton(jmol, 'load some_molecule.pdb', 'DNA'); would not even show up.

I think a better argument would be that if you used the jQuery framework, you could have a much richer user interface -- tabs, buttons of all sorts, flying images, etc. That, to me, would be a distinct positive, and I think some interesting examples using, say, tabbed applet panels (that work -- i.e. never use "display:none")  would be very interesting. (You know about never using display:none with an applet, right?)
Well fancy stuff is a nice side effect for jQuery, but that is not what I'm into here.

First, despite the convention, please don't use "jMol" -- we've had issues with this before and other  application. It should just be "Jmol". Please. Maybe jQuery-Jmol if you must start with a lower-case letter.
OK jQuery-Jmol it will be.

2. Get rid of document.write - it's a fast feature, but it forces developer to use inline coding. Instead I'd suggest to use native DOM methods for appending DOM fragments, or the nasty, but still easy inlineHtml or jQuery's append() or replaceWith();

That is, make all calls after the page has finished loading and the </body> tag is processed. Right? From


And then have all of JmolControls.js be implemented using jQuery. I would welcome that. I just would suggest not looking at all at Jmol.js. We need to move forward, not backward!

Well not only that, JmolApplet.js could be completely replaced with my jQuery plugin, as it's what my plugin does - it creates a Jmol applet and places a HTML code in the placeholder tag.

Gusts Kaksis