My favorite PyMOL settings
I often get asked how I generate the molecular graphics in my HX-MS and PIGEON-FEATHER papers. Here are my favorite PyMOL settings.
# basic display settings
set cartoon_loop_radius, 0.4
set cartoon_sampling, 10
set cartoon_transparency, 0
set line_width, 3
# ray tracing settings
set ray_trace_mode, 1
set ray_shadows, 0
set ray_trace_gain, 0.1
set ray_trace_disco_factor, 1
set ray_trace_color, black
# lighting and material settings
set antialias, 2
set specular, 0
set power, 0.0
#set power, 0.2
set ambient, 0.4
set direct, 0.45
set valence, 0
# space cmyk

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