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
set cartoon_ring_mode, 1
set cartoon_nucleic_acid_mode, 0
set cartoon_ring_color, red
set cartoon_ring_transparency, 0.5
set ray_trace_fog, 1
turn on “surface”
set surface_color, white
set transparency, 0.35