The pseudoatom business looks very cool. I'll have to try it out.
In the meantime, I wanted to mention that you certainly can make
transparent CGOs. Here's some code that I wrote to visualize dock
output in our lab. The files it reads in have lines that look like
junk x y z r junk temp junk
Pre 1.0:
fragment methane, mysph
remove hydro and mysph
alter mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph
Post 1.0:
pseudoatom mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph
Cheers,
Warren
_
From:
