PyMOL resources

PyMOL cheat sheet (2 dense pages, by R. Bryn Fenwick)

PyMOL tutorial & tips (4 pages, by Ross)

PyMOL basics (1 page, by Ross - largely redundant with the two files above)

Scroll down to get the text commands for this style:

The big chunk of commands below should produce a cartoon style similar to that shown above. Note that the transparency was applied to the foreground helices in Photoshop. I’m a PyMOL enthusiast, not a magician!

Main style commands:
hide
show cartoon
set bg_rgb, [1,1,1]
set cartoon_side_chain_helper, 1
set ray_shadow, 0
set stick_radius, 0.15
set cartoon_loop_cap, 2
set cartoon_smooth_loops, 1
set cartoon_loop_quality, 10
set cartoon_loop_radius, 0.16
set cartoon_rect_width, 0.3
set cartoon_fancy_helices, 1
set cartoon_fancy_sheets, 1
set cartoon_tube_radius, 0.4
set cartoon_ring_mode, 3
set cartoon_ring_width, 0.1
set cartoon_ring_finder, 1
set cartoon_ladder_mode, 1
set cartoon_nucleic_acid_mode, 4
set cartoon_ring_transparency, 0.5
set ray_trace_mode, 1
set antialias, 1

Notes:
• Use “ray ###,###” (numbers specify pixel width, height) to get your render.
• To fine-tune the size of the black outline, you can change the antialias parameter: 0 = wide line; 1 = medium line; 2 = thin line. Because the outline seems to be associated with a pixel width, the effective/apparent width (relative to the molecular features) changes as the pixel dimensions of your resolution changes (the ###,### above). Try a few different resolutions to find something that looks nice. You can also try the ray_trace_gain parameter (wiki link), which I find useful for sticks (less so for cartoon).
• The bottom two commands control the “cartoon” black outline that defines this look. It really slows down the rendering. If desired, you can omit those two commands when copying the text above, or you can turn it off via: set ray_trace_mode, 0 (wiki link).
• For classic nucleic acid bars: set cartoon_ring_mode, 0

Lighting & surfaces:
ray_texture (1 = matte)
spec_power                             default is -1; +1 is super bright light; -3 is infinitely low
spec_reflect                             default is -1; -2 helps give a matte look
specular_intensity                   1 is a lot, 0.1 gives a matte look
set light, [-4, -4, -10] this controls the location of the light in 3D space