From: Josh Vermaas (
Date: Fri Mar 08 2013 - 09:18:28 CST

Hi Andrea
The easiest way I could think of doing this would be to make a custom
material per atomselection. Under the graphics->materials menu, you can
make new materials, and if the "transparent" material is highlighted,
the new material made will have the same defaults as transparent, and
then you can tune the opacity for each material to your liking. Another
option would be to look at the other default materials, and see if any
of them would also fit your needs (glass1 looks alot like transparent to
-Josh Vermaas

On 03/08/2013 08:19 AM, andrea spitaleri wrote:
> Hi there,
> I am wondering whether in vmd we can set different opacity for
> different selection when transparent is used as material. I'd like to
> make 3 surfaces of a multidomain protein with different opacity but I
> could not find the way (if there is of course).
> thanks in advance
> and