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
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.

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4 Comments »

  1. You have some nice PyMOL posts. If you think the pages on pymolwiki.org 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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