Bob,
Thanks for all of your hard work on JSmol. What's happened in just a few months
is nothing less than amazing.
I've had the model kit bug ever since I found that I could make atoms in Chime
change color. Your Jmol efforts provided an opportunity to create a real
virtual model kit, and I'm convinced that JSmol is simply a opportunity to
expand this concept in new directions. For me, the shortcomings are simply
invitations to rethink old approaches, which in turn are really invitations to
play some more.
The link below points to the page that I'm using to experiment with JSmol as a
model kit. I have the bad habit of changing web page file names, but the
directory link below will always point to the JSmol model kit page:
http://chemagic.com/modelkit/
Thanks again for making this transition possible, seemingly just in time.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 13, 2013, at 2:29 PM, Robert Hanson wrote:
> Web page developers using the Jmol applet:
>
> Well, I'm sitting here wondering if the future of the Jmol applet is written
> on the wall, and it will soon become a historical artifact. As platforms shut
> out the Java plug-in, that certainly seems to be the case. If nothing else,
> we are instantly back in the land of only certain browsers being able to
> display a model. (Note that this concern has nothing to do with Java in
> general -- not the Jmol application, for instance -- just the Java web
> browser plug-in. That's an important distinction to keep in mind.)
>
> Time to summarize where we are, then, in terms of JSmol:
>
> Executive summary:
>
> JSmol/HTML5 is a faithful reproduction of Jmol/Java. It is the same code that
> is used to create both, so what you see in Jmol should also automatically be
> in JSmol. I can only think of one or two things right now that are not there
> -- background and ECHO images, for example. And minimization has not been
> optimized yet. A great example of how JSmol is being quickly picked up is
> what Otis Rothenberger is doing at chemagic.com. I'll let him point us to the
> pages he is working on. They look spectacular, and it is really very funny
> that without the logo, it's pretty hard to tell it's not Jmol itself.
>
> Installation of JSmol or conversion from a page that uses Jmol (especially if
> you have started to use the "JmolJS" library) is easy. Just download the zip
> file from https://sourceforge.net/projects/jsmol/files/release and unzip it.
> Following the examples, you need JSmol.js JSmolCore.js, JSmolApplet.js,
> JSmolApi.js and JSmoljQuery.js. Add JSmolControls.js if you are creating
> links and buttons and menus as was the case for Jmol. Then just add the j2s
> directory, and you are good to go.
>
> Full story:
>
> JSmol uses the Java2Script system to convert Java code to JavaScript within
> the Eclipse development environment. The system allows for idiosyncrasies of
> JavaScript to replace bits of Java when needed. The huge advantage of
> Java2Script over anything else I considered (Google Web Tool Kit, for
> instance) is that, being a faithful reproduction of the core Java package,
> Java2Script allows for extensive Java-like debugging, lets us adapt the Java
> package for faster JavaScript performance, and, most importantly, keeps us on
> one development path. JSmol hasn't diverged from Jmol -- it IS Jmol, just
> repackaged on the fly into JavaScript. The same code still generates the Jmol
> Java applet and the Jmol Java application. Any development of JSmol is still
> development of Jmol.
>
> I have been working on JSmol since late August -- about 4 1/2 months now. In
> that time I have done a significant amount of refactoring of the Jmol code as
> well as some adapting of the Java2Script libraries to make the magic happen
> and to increase overall performance (both in Java and JavaScript, actually),
> and that has paid off considerably.
>
> Yes, JSmol is slower than Jmol. My tests suggest that JavaScript is about
> 5-10 times slower than Java in many tasks.
>
> No, you can't do everything in JSmol that you can in Jmol.
>
> Some processes are going to be too slow to be useful. Particularly with
> proteins and specifically with molecular surfaces (as opposed to
> solvent-accessible surfaces), in cases of huge models, and particularly with
> large canvases (1000+ pixels width or height) there may be some issues. We'll
> have to see how that goes.
>
> But what you can do in JSmol is pretty amazing. You can read all the files
> that Jmol reads. You can do all the scripting that Jmol does. You can create
> all the buttons and links and such that you are used to creating for Jmol.
> All of the rendering capability of the Jmol applet is there (other than the
> couple of TODO issues mentioned above). We have a console and a popup menu.
>
> There is no distinction in JSmol between "signed" and "unsigned" -- consider
> it signed. There is a little PHP piece that allows binary files to be read
> and image and state files to be created, including PNG, PNGJ (which serves as
> an image, a ZIP file, and as input back into JSmol or Jmol as a 3D model),
> and JMOL (i.e. ZIP) files.
>
> I am comforted by the fact that nothing else comes even close to the sort of
> capabilities that we have in JSmol already. The closest I can think of is
> ChemDoodle, which has a smaller footprint than JSmol. It was a great early
> experiment in the possibilities of HTML5/WebGL, and it may have some
> potential, but, at least in my opinion, it is currently quite limited in
> providing anything more than 3D "eye candy" to a page. (If that is all the
> page needs, and you are happy with the licensing, go for that. You do not
> need JSmol.) To my knowledge ChemDoodle's protein visualization is limited to
> WebGL, which pretty much means no surfaces and only limited support for
> cartoons and such. There is no high-level scripting language as there is in
> JSmol, so doing anything of any sophisticated nature at all will require
> expertise in JavaScript and a pretty full understanding of the ChemDoodle
> model. And it has plenty of limitations with respect to model size, just like
> JSmol. Nothing surprising there, I think.
>
> There is still plenty of testing of JSmol that needs to be done to get it to
> the level of widespread platform consistency that we saw in Jmol. But we are
> very close to that prize, I think.
>
> Bob Hanson
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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