My software notes

October 22, 2006

PyMOL Fancy DNA helix and filled Rings

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

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)

3 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


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