VMD-L Mailing List

From: Sabine Reisser (sabine.reisser_at_kit.edu)
Date: Fri Feb 15 2013 - 08:57:40 CST

Dear VMD users and developers,

I'm trying to generate a nice picture of a molecule (in licorice) within
its transparent electrostatic potential surface (surf, material
diffuse). I'm using the GLSL render mode, and the surface generally
looks nice and smooth.
I've played with the opacity settings in tk console using
material change opacity Diffuse "..."
but the molecule inside the surface generally disappears when I take an
opacity value higher than 0.5. I can still see the surface and it's
transparent, but it's empty. This problem appears only in GLSL render mode.

Also, the surface in GLSL mode looks stainy if the opacity is below 1
(independent of the material). I suppose this is because of light
reflection and shadows inside the molecule, but I would rather get rid
of it.

It would be great if somebody could comment on these issues.

Thanks for reading!

Cheers
Sabine