I think Jmol should never be playing with its own scripts that way unless you are talking about doing this specifically in the applet and specifically using JavaScript. If we need to copy the object, we just copy the object. We can copy an isosurface pretty easily without resorting to running scripts, I think. In fact, we could just link one to the other and use the same vertex data. Why copy?

Wouldn't it be way better just to deliver half of the isosurface in the opaque pass and half in the translucent pass? I think this is just a variant on "isosurface slab...." that rather than not displaying some subset of polygons instead renders them translucent. Not a particularly difficult thing to implement. We'd just render one portion of the polygons in the translucent pass and one portion in the opaque pass.

I still need to see what you are thinking this would look like in terms of a script command. Why don't we spend a few days working all that out first, then do the implementation. You know what you want, I think, and once I see that, I can think about ways to implement it. Something like this, perhaps:

isosurface slab translucent x=3  # ghostified along a plane
isosurface slab translucent 0.3 within range -100 0 # ghostifies the negative values
isosurface slab translucent 0.8 within 5.0 @3    # new way to do "{atomno=3}"


On Thu, Jul 14, 2011 at 9:34 AM, Jonathan Gutow <gutow@uwosh.edu> wrote:
I think this is for Bob.

Inorder to create a ghost isosurface (or any other shape), I need to duplicate the shape and change some of the rendering parameters.  The cleanest way seems to be to make a copy of the command that created the surface and change just the name and relevant rendering parameters.  This way the new surface is added to the Jmol state in the normal way.  So, I was investigating what I can get back using the viewer.getProperty() call.

I used a call like:  Object shapeInfo = viewer.getProperty("Object", "ShapeInfo", null);

I gather this is just a little more general than using calls to viewer.getShapeProperty.

Anyway, my question is this.  The returned object is missing the Jmol State version of the isosurface recreation command, is there another way using some version of these "getProperty" calls to access this?  The "title" appears to have the basic (user entered) command, but I would prefer to work with the Jmol State version, because they are more complete and I believe will reduce the chances of having to update my code if defaults or parameters change.


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