QuteMol allows production of nice realistic molecular pictures. PyMOL could do similar things albeit results are not strictly equivalent. Here is an example taken from the PyMOL wiki that produced the picture above.
fetch 1BTA
set_color oxygen, [1.0,0.4,0.4]
set_color nitrogen, [0.5,0.5,1.0]
remove solvent
as spheres
util.cbaw
bg white
set light_count,10
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue
ray 1200, 1200
