Hi Henry!
I did a little bit of work on the VRML and X3D exporters, so I feel engaged in
this.
I'm surprised at the difference you describe.
Is by any chance your surface (orbital) model loaded from a jvxl file, or is it
created on top of the atoms?
I had some experience when a molecular isosurface, loaded without atoms,
got a weird scale in Jmol.
I've just run a small test
1. alanine balls and stick
2. balls and stick + molecular surface (colored by MEP)
3. molecular surface only (after hiding all atoms from #2)
VRML file sizes:
1= 6 kB
2= 287 kB
3= 282 kB
So the data load matches. I checked the files and general parameters are
the same, just the relevat lines for atom shapes added or missing.
Then I uploaded them to Shapeways (nice service I didn't know of, thanks!)
1= 0.4 x 0.3 x 0.2 cm, Density: 7.58%, $1.50
2= 0.7 x 0.5 x 0.5 cm, Density: 42.90%, $1.62
3= 0.7 x 0.5 x 0.5 cm, Density: 42.90%, $1.62
So (1) I don't suffer your problem, (2) my model is really tiny!
So a scaling option would be great.
Maybe I could choose "inches" when uploading rather than mm to get a
bigger one... Yes! that brings it to
2= 18.0 x 13.1 x 13.6 cm, Density: 42.78%, $972.51
Still, way large an increase. We need scaling.
I see there is a "scale" parameter in VRML specification --which Jmol is not
using-- Now the question is how to understand it.
I tried to manually insert a scale in the wrl file. Result: an error.
Another try: success!
scaled to 50% and uploaded as inches
2= 9.0 x 6.5 x 6.8 cm, Density: 42.78%, $135.13
The trick:
1- open the WRL file in a text editor
2- find the first instance of "transform", e.g.
Transform{children Transform{translation -.073 .394 .076
3- add scale after translation (or before it I guess), like this:
Transform{children Transform{translation -.073 .394 .076
scale 0.5 0.5 0.5
4- save
Now back to the surface vs. ball and stick difference
I saved my molecular isosurface to disk (jvxl). Then zapped and loaded the
isosurface only. Exported to VRML (call it #4).
It looks rather smaller in my VRML viewer application than #2 or #3.
I added no scaling here.
Uploaded to Shapeways as inches. This is the result:
4= 18.0 x 13.1 x 13.6 cm, Density: 42.79%, $972.52
so no difference to the atoms + surface file:
2= 18.0 x 13.1 x 13.6 cm, Density: 42.78%, $972.51 (without rescaling)
Funny they offer color for the surface but not for the ball and stick model.
Why would that be so?
Great fun!
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