On Tue, Jan 15, 2013 at 2:25 PM, Kevin Theisen <ke...@ichemlabs.com> wrote:
> Bob,
>
> To answer your questions:
>
> This is really an argument of semantics, with the ChemDoodle Web
> Components, we would do something like the following.
>
> var selected = myCanvas.select(10, 20);
> myCanvas.center(selected);
> myCanvas.repaint();
>
I see repaint() at http://web.chemdoodle.com/docs/api. Are center() and
select() there and I just don't see them? How does the select() function
know that's a range of PDB residue numbers and not some sort of atom IDs?
>
> Instead of using Jmol script and the Jmol compiler, it would just be pure
> Javascript with the ChemDoodle Web Components API.
>
There is no "Jmol compiler" but I know what you mean. I'm very interested
to see how that plays out.
>
> But let me describe a little more about what the ChemDoodle Web Components
> library is. It was devised as a portable API to build scientific
> interfaces. This may include structures, reactions, spectra and 3D. It may
> also include other things that we have not done yet, such as graphs and
> vector maps. It was not created to compete with Jmol. The ChemDoodle Web
> Components library is also a framework, which is different from most
> graphical solutions like Jmol, which are applications. Jmol and other
> applications are prebuilt to define how a user uses them.
>
That is a very strange thing to say about Jmol! Of all the software we have
ever seen on the web, surely Jmol is about as non-prebuilt as they come.
The value of Jmol is specifically in that it can be adapted easily to any
number of different situations. That's what has made it so ubiquitous.
>
>
> Ok, moving on, let's discuss WebGL. WebGL has been the biggest restraint
> for our development of advanced 3D scientific graphics. It is a very
> powerful technology, but its support across browsers (both mobile and web)
> have progressed at a snail's pace. We first started working with WebGL in
> 2009. In early 2011, Chrome and Firefox both enabled it. Further support
> has remained stagnant until last week when it was announced WebGL is coming
> to Android (
> http://blog.tojicode.com/2013/01/get-webgl-working-on-android-chrome-beta.html).
> I would have to bet that WebGL is coming to iOS this year as well. With
> that being said, WebGL is supported in all desktop browsers today. Firefox
> and Chrome support it by default, you can turn it on in Safari and Opera,
> and for IE6-9, there is Google Chrome Frame. That brings us to the second
> restraint with WebGL, hardware support. As with all hardware accelerated
> technologies, you have to take into account the hardware. This is
> especially important with a web technology, because security is infinitely
> harder. So there are blacklists from the browser vendors to restrict WebGL
> for given graphics cards. Browser vendors are working through these issues
> though, and last we checked, the blacklists are shrinking. This is a good
> thing, because the browser vendors are ensuring that WebGL is a safe
> technology.
>
>
That's a very clarifying point. I guess we'll see. In the mean time, we
have HTML5. By the way, there have been some very interesting blogs about
the danger of HTML5. It may be next.
> I don't keep track of all the open projects on the internet, we don't know
> all of those that exist, but here are some that caught my attention:
>
> From the Polymer Science Learning Foundation -
> http://chemsrv1.uwsp.edu/advanced/index.html
>
OK, so this is an example of simply popping in a model.
> Seqcrawler - http://www.biomedcentral.com/1471-2105/13/175/abstract
>
I wasn't able to find the 3D viewer at their site
http://seqcrawler.genouest.org/seqcrawler/, but there was a mention of it
as "experimental" in the paper, I see.
http://doctorbrookschemistry.net/
Are you referring to the "3D model" page? Or do you see that elsewhere on
the site?
http://www.ch.imperial.ac.uk/rzepa/blog/?p=5881
Yes, Henry has been experimenting with it.
http://molecularmodelingbasics.blogspot.com/2011/05/interactive-chemistry-ebooks.html
And of course, one of our proudest collaborations, Jmol -
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
Thank you -- Yes, that was a very interesting experiment. Unfortunately,
due to the limitations of ChemDoodle and the licensing issues, that one's
been discontinued. It was an early experiment to see if ChemDoodle could
fit into the JmolJSO idea, and it worked reasonably well, but it was so
limited, it didn't make a lot of sense to continue with that once we got
HTML5 and WebGL working with JSmol.
But I see your point, I think. If you just need a quick port with a 3D
model in it, and you are comfortable with the licensing, ChemDoodle can do
a decent job of it. Because of the limitations of WebGL coverage, I only
see "future" possibilities for macromolecules in relation to WebGL, even
with JSmol, and even then there are going to be huge memory issues if you
ever do get surfaces going, but as you say, someday Apple may see the light
and give us access to WebGL on the iPad. That would certainly open up some
new possibilities.
Bob
--
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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