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:
ray
Then export the resulting image to a .png file.
Happy Pymol'ing
set antialias,2
ReplyDeletehelps a bit as well :).
png filename.png, ray=1, dpi=1200
saves the ray-traces image in 1200 dpi
Nice, will try :)
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