PyMOL (I am using 2.3 now) has a “pymolrc” option that users can pre-define the software environment. For example, I like to make see while background instead of black. I like to save all fetched PDB in a collection folder.

One can edit the pymolrc at File -> “Edit pymolrc”

Here is my pymolrc

# save fetched PDB files here
set fetch_path, /home/kpwulab/PDB 

# set background color white
bg white

set ribbon_width, 8
set antialias,2
set cartoon_fancy_helices,1
set cartoon_discrete_colors, 1
set cartoon_side_chain_helper, 1
set ray_trace_mode,1
set depth_cue,0
set ray_trace_fog,0
set ray_opaque_background,0
set defer_builds_mode, 3