Tuesday, December 10, 2013

Beautiful rendereing of small molecules in Pymol

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:

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 oritented the molecule to the position you want in your picture, type in the console:


Then export the resulting image to a .png file.

Happy Pymol'ing


  1. set antialias,2

    helps a bit as well :).

    png filename.png, ray=1, dpi=1200

    saves the ray-traces image in 1200 dpi