Getting ready to submit a publication of my FragBuilder paper to PeerJ, I had to make several pictures of peptides and pictures to illustrate dihedral angles in the 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 that I added the torsion angles in LibreOffice Draw manually.
The Pymol commands to make the above figure are:
color grey05, elem c
set ray_trace_mode, 4
Once you have oritented the molecule to the position you want in your picture, type in the console:
Then export the resulting image to a .png file.