Povray is a is a high-quality tool to create 3d graphics. Here is my notes on rendering molecules and coarse-grained models.
Ray tracing:
global_settings {
radiosity {
count 60
always_sample on
recursion_limit 2
error_bound 0.8
}
}
Texture:
texture {
pigment {
bozo color_map{[-2 rgbt <0.3, 0.3, 0.3, 0.0>][1.0 particleColor]} scale 0.25
}
normal { bumps 0.3 noise_generator 2 scale 0.08 }
finish { specular 0.8 roughness 0.2}
}
Result:

As marked by blue square, the boto
controls the dark spots on the sphere, and bumps
creates the look of rolling hills. The specular
keyword in a finish statement produces a highlight, which more closely resembles real specular reflection and provides a more credible spreading of the highlights occurring near the object horizons.