Getting ready to submit a publication of my FragBuilder paper to PeerJ, I had to make several pictures of peptides and figures to illustrate dihedral angles in proteins.

Personally, a little bit of me dies whenever I see a screenshot from GaussView in a publication. I used PyMOL to make the ray-traced 3D models. One example is shown below, and I think it came out pretty great.
Note: I added the torsion angles in LibreOffice Draw manually.

The PyMOL commands to make the above figure are:

load my_molecule.xyz
color grey05, elem c
bg_color white
preset.ball_and_stick(selection='all', mode=1)
set ray_trace_mode, 4

Once you have oriented the molecule to the position you want in your picture, type in the console:

ray

Then export the resulting image to a .png file.

Happy PyMOL’ing!