Examples of nucleic acid cartoons

pymol version info

The various new nucleic acid display settings for PyMol 0.99 listed below were produced using version 0.99 beta 29 on Windows XP with an arbitrary B-form DNA molecule. Higher values could be set for each setting but appeared to yield the default representations.

default settings

The defaults give a phosphate backbone with single sticks passing across the full width of the base plane.

set cartoon_nucleic_acid_mode, 1 # backbone follows phosphates
set cartoon_ladder_mode, 1 # sticks from backbone into nucleotide
set cartoon_ring_mode, 0 # no nucleotide rings
set cartoon_ring_finder, 1 # ribose and base rings (not displayed as ring mode 0)

default view

cartoon ring modes

set cartoon_ring_mode, 0 # no nucleotide rings
set cartoon_ring_mode, 1 # filled rings extending to outside edge of bonds
set cartoon_ring_mode, 2 # filled rings extending to inside edge of bonds
set cartoon_ring_mode, 3 # filled rings with bonds as thicker lines

cartoon_ring_mode,0

cartoon_ring_mode,1

cartoon_ring_mode,2

cartoon_ring_mode,3

all with defaults: cartoon_ladder_mode,1   cartoon_nucleic_acid_mode,0   cartoon_ring_finder,1

cartoon ladder modes

set cartoon_ladder_mode, 0 # no ladder
set cartoon_ladder_mode, 1 # with ladder, as stick (if ring mode 0) or link to ring (if rings)

note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0

cartoon_ladder_mode,0

cartoon_ladder_mode,1

all with: cartoon_ring_mode,3   cartoon_nucleic_acid_mode,0   cartoon_ring_finder,1

cartoon nucleic acid modes

set cartoon_nucleic_acid_mode, 0 # backbone follow phosphates (red)
set cartoon_nucleic_acid_mode, 1 # backbone follows C4' of ribose (green)

cartoon_nucleic_acid_mode,0

cartoon_nucleic_acid_mode,1

all with: cartoon_ladder_mode,0   cartoon_ring_mode,3   cartoon_ring_finder,1

cartoon ring finder

set cartoon_ring_finder, 0 # no ribose, base (or ladder)
set cartoon_ring_finder, 1 # ribose and base ring
set cartoon_ring_finder, 2 # base ring only

cartoon_ring_finder,0

cartoon_ring_finder,1

cartoon_ring_finder,2

all with: cartoon_ladder_mode,1   cartoon_ring_mode,3   cartoon_nucleic_acid_mode,0