[Jmol-developers] RFE: animations, semantic zooming/specification and cross annotations, references and linking ...

[Albretch M. <lb...@gm...>]

 Hi,
~
 I am impressed with JMol but your browser applet examples (e.g.)
~
 http://www.worldofmolecules.com/3D/dna_3d.htm
~
 http://chemapps.stolaf.edu/pe/protexpl/htm/top.htm?id=1d66&&&chpa=true
~
 to me look more like a viewer, than an actual content browser per se.
~
 I'd wish it would include animations, semantic zooming/specification
(from/to atomic, molecular, cellular, multi-cellular/biological,
functional levels), and cross annotations, references and linking.
~
 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, ...)
~
 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 ...), ...
~
 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
~
 Can you point me to any such or similar examples?
~
 I notice some users have requested annotations and I read through
some threads, among them: "Record animation option within Jmol"
~
 http://www.mail-archive.com/jmo...@li.../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
~
 What I am talking about may sound senseless or esoteric for you, but
for example I coded myself the references and linking part that I
mentioned for a representation of Euclid's Elements in which the
textual explanations, formulaic representations and the graphical
rendering were linked, so if a student was reading the textual part
the could hover the mouse over it and see how it relates to the
graphical representation.
~
 I am a theoretical Physicist (group theory of solid-state/fairly well
trained in Chemistry) and a professional Java programmer. I could dive
into your library if you find my RFE valid/meaningful and feel like
culturing them. I am (like anyone else) currently busy doing more than
one thing, so it all comes down to logistics:
~
 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. How fast would you answer
"newbies" questions? ;-)
~
 thank you
 lbrtchx