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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