Dear Albretch,
I think you properly describe Jmol as a viewer rather than a content
browser. Our mission is to provide methods of visualization primarily for
molecular systems and primarily for the web. "Primarily" because Jmol has
many capabilities that go beyond visualization, and its use is not
restricted to the web or to molecules, per se. So, for example, Jmol can be
used on a server to do calculations instead of visualization. Jmol can be
included in other more complex Java packages. Examples include WebMO [
http://www.webmo.net] and Concord Consortium's Molecular Workbench [
http://mw.concord.org]. Jmol is used for the online Sage Notebook
mathematics package [http://www.sagenb.org] to render three-dimensional
representations of mathematical functions. Jmol can render electron
microscopy data, which is often one level up from molecular.
In the context of the web, Jmol is most powerful specifically because it
does NOT "include" some of the things that you mention below. This may seem
strange to say, but it is a matter of philosophy. Much of what you describe
is possible with Jmol, but is not "included" in Jmol. Unlike other programs
that are stand-alone monolithic entities, Jmol is highly modular and can be
smoothly integrated into contexts to provide a visualization component.
There are hundreds of examples of such. I direct you to the Jmol Wiki [
http://wiki.jmol.org/index.php/Websites_Using_Jmol]. The key is an extremely
powerful programming interface that allows full control of a visualization
from user-directed JavaScript on a web page.
So, with respect to some of your ideas:
~
> animations (animated reactions (probably based on known chemical
> bondings)): say, you want to watch reactions as they happen (plain
> chemical reactions on a physical level, transcription in eukaryotic
> cells, ...)
>
Certainly there are many examples of Jmol being used for animations of
chemical reactions. That is one of the tasks we do best. One can animate
reactions in Jmol so that the user can stop, start, and investigate the
reaction from any angle while the animation proceeds. In addition, one can
use Jmol to create a series of JPEG or PNG images that can be passed to more
specialized editing programs for the production of actual movies, such as we
have at [http://www.youtube.com/watch?v=AilBZeeeETk]. Making a movie is far
more than simply sticking a bunch of images together, and it seems
reasonable to us to leave that sort of operation to packages that do that
specific task, such as Windows Movie Maker.
> ~
> semantic zooming/specification: you would zoom in/out to actually see
> how related molecules and cells interact (molecular binding needs
> energy what would be the effect of their lack ...), ...
>
No one to date has achieved interactive semantic zooming. Wouldn't that be
fun! All such efforts to date involve professional animation software such
as Maya. So there is no interaction by the user there, but the results,
though a passive experience for the user, are stunning. It's certainly an
interesting idea.
> cross annotations, references and linking: while you read a related
> text by selecting any part of the text (say something you don't
> understand) the corresponding part on the graphical representation
> will be shown/zoomed and/or highlighted
> ~
>
People do this all the time. It's one of our nicest features. Extremely
simple to implement. See, for example, Proteopedia [
http://proteopedia.org/wiki/index.php/Hemoglobin].
> ~
>
> http://www.mail-archive.com/[email protected]/msg12964.html
> ~
> I think there is an easier way to do that. ("easier" if you are using
> Linux ;-)) you could simply do a screen capture of a window of your
> screen and stream it as an mpg file and even record your own voice
> with a standard microphone
>
Right, there are certainly hacks like that that would get the job done.
Another option is to run Jmol within PowerPoint and use the capture
facilities there, I think. That said, the capability of producing video with
voice-over would be fabulous. I think it would be a great challenge and
would take some research to see if a PC can handle it in real time. Most
likely one would not use the applet for this and would instead include this
as an option with the Jmol application.
~
> Do you have documents describing the inner working of your software?
>
Even if you are a good developer you will have questions when you
> don't have a mental map/thorough understanding of the inner working
> and design philosophy behind the code.
Don't I know it! Sometimes it takes me some time just to remember what I
myself did when I need to get back into the code and augment it in some way.
I guess our philosophy on this is that it is important to make the actual
coding as transparent as possible. With modern tools such as Eclipse, one
can relatively quickly walk through a process and learn what is going on. In
certain cases there are voluminous programming notes, and we try in all
cases to provide references to the literature when we utilize known
algorithms. But this is a volunteer effort, and our priority has to be
functionality over metafunctionality. Certainly the scripting language
itself is well described at http://chemapps.stolaf.edu/jmol/docs
> How fast would you answer
> "newbies" questions? ;-)
>
generally within minutes to hours, depending upon the volume and the time
zone.
Bob Hanson
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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