set sphere_transparency is used to adjust the transparency of spheres!
set sphere_transparency, 0.5
set sphere_transparency=0.5, selection
Where 1.0 is invisible and 0.0 completely solid
These images were made through the following script:
fetch 1ifr; color wheat; hide; show spheres; color red, i. 506-509; color marine, byres all within 5 of color red; set sphere_transparency,0.5,color marine;