If you are doing this in JavaScript, I would grab the state script and strip
out the isosurface command from it that was used (we could add some comments
to define it's first and last lines exactly), change the ID, and then run it
as an inline script; if doing this in Java, you have access to any
On Jul 2, 2011, at 2:36 AM, Robert Hanson wrote:
Yes, the bounding box is in molecular coordinates. So except for the ghosting
-- which I actually do think is done best by displaying two surfaces --
that's no problem with the applet, because you can just deliver it any way
you want to. I
On Thu, Jun 30, 2011 at 8:50 AM, Jonathan Gutow gu...@uwosh.edu wrote:
So I am still at my original question, which is will the boundbox
coordinates always be parallel to the molecular coordinates?
Yes, the bounding box is in molecular coordinates. So except for the
ghosting -- which I
well, the molecular coordinates are just the molecular coordinates. This
slicing is by them, right? Not the screen coordinates? There are three
coordinate systems:
-- molecular coordinates
-- relation of those by rotation to the original view (the orientation
quaternion/matrix)
-- translation
By the way, you asked about the possibility of duplicating an isosurface so
there was a translucent shadow. Since rendering is a two-pass system, a
better way...
... to do that might be to set a flag to render the translucent pass without
slab and the opaque one with. Something on that order
Last comment first.
On Jun 30, 2011, at 1:10 AM, Robert Hanson wrote:
By the way, you asked about the possibility of duplicating an isosurface so
there was a translucent shadow. Since rendering is a two-pass system, a
better way...
... to do that might be to set a flag to render the
I try to answer your questions below. In summary, now that you've changed the
isosurface slab command so that it can be done after the surface is defined I
am mostly concerned with building a GUI that is intuitive enough that people
don't have to understand the details of the isosurface and
As I am working on figuring out what I have to track for a GUI to control
slabbing/slicing, I have encountered the issue that the coordinate system for
the molecule and the viewing space are not always the same. Do I have to worry
about relative rotations of these axes or just the offset of
