Is there a way for browsers to read and display cml?
I see
http://cvs.sourceforge.net/viewcvs.py/jmol/Jmol/samples/cml/SN1_reaction.cml
but what would you do with that?
Bob Hanson
Miguel wrote:
The CML syntax currently used in Jmol is:
<list dictRef="jmol:animation">
<molecule id="FRAME1"/>
<molecule id="FRAME2"/>
<!-- etc -->
</list>
I guess the molecule element could use a @dictRef="jmol:animationFrame"
See for example CVS samples/cml/SN1_reaction.cml
Yes ... I had forgotten that this works :-)
In principle one can animate the chemistry (molecular structure) and
also
the visualisation (display styles, visibility, opacity, etc.)
opacity is something that scares me.
Here are some
suggestions and I'd be grateful for what Jmol can do at present and
would
like to do in the future. I am using molecule, atom and bond as the
primary
objects, though clearly with graphical objects (boxes, spheres, etc.)
there
are other possibilities.
Q: What would be the purpose of having general graphical shapes as part of
a reaction?
The display properties are informed by SVG
which
can animate most CSS attributes and several others. We have been
animating
reactions using 2D SVG graphics and currently use many off:
graphical object (and text):
colour, visibility, position, rotation, opacity
molecule:
colour, visibility, position, rotation, opacity, velocity,
surface
atom
colour/style, visibility, opacity
x,y,z
velocity
elementType (not common, but possible in free energy
perturbation)
bond
existence (important for reactions. We need to be able to
insist
on bond depiction, regardless of covalent radii)
display style (transition from solid to dotted, etc.), colour,
radius, etc.
order (double may change to single, etc)
position. It may be useful for bonds to "swing" from one part
of
connected atoms to another (represents curly arrows in reactions)
The SVG animations give people a new and often exciting feel about
chemical
reactions. If Jmol can do this in 3D it will be incredible. I suspect
that
much of it is already there in some form.
I think Miguel can best respond to these... I think most is implemented
except for opacity, surface and 'curly arrows'...
I think that Egon is correct ... most of these things can be done.
Q: what is a 'curly arrow' ?
However, there is currently no mechanism to specify these attributes as
part of the file format. That is, within the molecular model file there is
no way to specify atom attributes like color or size. I do not think it
would be difficult to do, but there is something about it that makes me
uncomfortable. I will need to think about that.
In any case, we will only consider adding this type of 'extended animation
support' post the official v10 release.
Miguel
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
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"Imagination is more important than knowledge." - Albert Einstein
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