Pymolrc

When Pymol launches, it will read custom settings and functions from a .pymolrc file.

On a linux-type system, this file will be located in /path/to/home/.pymolrc.

An example of a .pymolrc file is:

# this will run the script in the specified location
run /path/to/home/pymol/load_sep.py

set movie_loop, 0
set two_sided_lighting, 1

set label_size, 60
set label_outline_color, 1
set label_color, 0
set label_position, [0, 0, 10]

# for images:
#   antialias =1 smooths jagged edges, 0 turns it off
set antialias = 1

#   stick_radius -adjust thickness of atomic bonds
set stick_radius = 0.3

# Below is an function that can be used to turn on special settings 
# when you are creating an image for publication: 
def imageSettings():
     set depth_cue = 1
     set two_sided_lighting = 1
     set ray_interior_color = grey20

cmd.extend('imageSettings', imageSettings);

See Also

Launching PyMOL