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