My software notes

October 22, 2006

PyMOL Fancy DNA helix and filled Rings

Filed under: pymol/ molmol — kpwu @ 3:12 am

<Update on July 27, 2011: New post of better DNA image can be read at here>

The PyMOL author provided a very good script to present DNA structure in fancy helix and filled rings without install the Nuccly plugin.

Here is an example (figure) and the script :
the three DNAs are ordered as A-form/B-form/1BNZ DNA with same sequence
all.png

set cartoon_ring_mode, 1 (or 2 or 3)
set cartoon_ring_finder, 1 (or 2 or 3 or 4)
set nucleic_acid_mode, 0 (or 1 or 2 or 3 or 4)

set cartoon_side_chain_helper
rebuild

set cartoon_ring_transparency, 0.5

set cartoon_ladder_mode, 0 or 1

set cartoon_ladder_color, color-name
set cartoon_nucleic_acid_color, color-name

cartoon oval
set cartoon_oval_width, 0.8

cartoon rect

cartoon dumbbell
set cartoon_dumbbell_width, 0.4
set cartoon_dumbbell_radius, 0.4

Another case (1BNZ), facny DNA representation and transparent surface to see the the contact between two molecules

complex (dna-protein)

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6 Comments »

  1. Lovely images. When I tried the script above with PyMOL v. 1.0r2 I saw no changes to the structure. Also, the setting ‘nucleic_acid_mode’ may have been replaced with ‘cartoon_nucleic_acid_mode’. Any thoughts?

    Thanks!

    Comment by m — April 9, 2008 @ 11:07 am | Reply

  2. Hello m,

    So far, I still stick on pymol 0.99 not v1.0+. I don’t have any idea how v1.02r2 doesn’t work as well as v0.99. I will try to get v1.0+ and test the script ASAP.

    Comment by kpwu — April 24, 2008 @ 6:48 am | Reply

  3. Dear PyMOL experts,

    Does anyone have a script that will render a PyMOL cartoon so that it looks like a MOLMOL picture; i.e. the red and yellow helices etc.

    It would be much appreciated

    David

    Comment by David — January 15, 2009 @ 6:19 am | Reply

  4. Hello kpwu,

    great work! very fine screenshot showing DNA abz forms. it’s very hard to find such a picture, i have been preparing a crystallography script for students and i’m stuck because of not having this picture. I tried the script but no changes were seen in the structure. If you have any pymol session of these 3 dna forms, maybe a bit longer in base pair I would be very grateful!

    Kindest regards,
    Andrzej

    Comment by Andrzej — December 6, 2009 @ 1:56 pm | Reply

  5. Andrzej,
    Unfortunately, I don’t keep the pymol section files. This picture was made years ago and I didn’t keep the old file while I changed to another macbook pro. I am sorry for late reply.

    Comment by kpwu — January 25, 2010 @ 10:40 pm | Reply

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