[PyMOL] example of DNA

Several private emails request me to show some examples of DNA/RNA using PyMOL. I am not familiar with commands related to nucleic acids in PyMOL because I never have chance to study DNA/RNA. I made some posts few years ago just for fun.

Here is a step-by-step re-cap I make followed by my old post.

PyMOL: 1.3 on Mac OS 10.6.5

DNA template: PDB code 2L8Q

beginning point: using “default cartoon” to show the duplex B-form DNA

set cartoon_nucleic_acid_color, yellow
cartoon oval

set cartoon_ring_mode, 1
set cartoon_nucleic_acid_mode, 0
set cartoon_ring_color, red
set cartoon_ring_transparency, 0.5

set cartoon_oval_length, 1.6
set cartoon_oval_width, 0.8
set cartoon_ring_width, 0.5

set ray_trace_fog,0
ray

set ray_trace_fog, 1
set ray_trace_mode,2
ray

turn on “surface”
set surface_color, white
set transparency, 0.35

Differences of “cartoon_nucleic_acid_mode” are shown at here.