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Pymolrc
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When Pymol launches, it will read custom settings and functions from a .pymolrc (windows: pymolrc.pym) file.
In windows put file under "C:\Users\YOU\pymolrc.pym".
On a Unix/Linux-type system (including Mac OS X), 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
# set fetch_path
set fetch_path, /your/fetch/path
To reload .pymolrc file (e.g. after editing .pymolrc, or after running reinitialize), use:
@~/.pymolrc