My software notes

July 26, 2011

[PyMOL] example of DNA

Filed under: pymol/ molmol — kpwu @ 4:41 pm
Tags: ,

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

set ray_trace_fog, 1
set ray_trace_mode,2

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

Differences of “cartoon_nucleic_acid_mode” are shown at here.



  1. You have some nice PyMOL posts. If you think the pages on are lacking for these sorts of things, you should consider adding to them.

    Comment by Michael Lerner — July 26, 2011 @ 9:28 pm | Reply

    • I will try. Thanks for suggestions, Dr. Lerner.

      Comment by kpwu — July 29, 2011 @ 6:00 pm | Reply

  2. […] <Update on July 27, 2011: New post related to DNA image can be read at here> […]

    Pingback by PyMOL Fancy DNA helix and filled Rings « My software notes — July 27, 2011 @ 3:19 pm | Reply

  3. […] up previous post, here shows several modes available in PyMOL to display the ribbon/chain of […]

    Pingback by [PyMOL] DNA–example II « My software notes — July 28, 2011 @ 6:09 pm | Reply

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