My software notes

July 28, 2011

[PyMOL] DNA–example II

Filed under: pymol/ molmol — kpwu @ 6:09 pm
Tags: ,

Follow up previous post, here shows several modes available in PyMOL to display the ribbon/chain of DNA/RNA.

Example molecule: B-form DNA PDB code:  2L8Q

Running version, PyMOL 1.3 (x11 version on MacOS 10.6)

The previous version use “oval” to show the ribbon of DNA. Here are some other ways to show the ribbon:

1. default ribbon shown by cartoon (“tube” mode)
default radius of tube mode

set cartoon_tube_radius, 1

2.  The  “oval” mode

cartoon oval
set cartoon_oval_width, 0.3
set cartoon_oval_length, 1.2

3. The “rect” mode:

cartoon rect
set cartoon rect_width, 0.5
set cartoon rect_length, 2

combined with addition command (molecule rotated):

cartoon arrow

4. The “dumbbell” mode:

cartoon dumbbell,
set cartoon_dumbbell_width, 0.3
set cartoon_dumbbell_length, 1
set cartoon_dumbbell_radius, 0.35

In most protein structures shown in papers, the helices and sheets are always colored in two colors. We can use “cartoon_highlight_color” to create such effect on DNA,too. Here is the example:

set cartoon_highlight_color, navy
set cartoon_nucleic_acid_color, palecyan

2012 May 24, new post about different colors for the rings.



  1. Hi, do you know how to make images like in this page:

    Comment by Uttam — August 30, 2011 @ 1:46 pm | Reply

  2. […] image above can be drew followed by steps in my earlier post, which shows single color of the nucleotide rings and […]

    Pingback by [PyMOL] different colors of nucleic acid rings « My software notes — May 24, 2012 @ 12:55 am | Reply

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