Examples of nucleic acid cartoons

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, 0 # backbone follows phosphates; actually Pymol itself uses setting '4' as default
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 since ring mode 0)

default view

Cartoon ring mode

Settings

set cartoon_ring_mode, value

value	effect
0	stick from backbone atom to N1 of purines and N3 of pyrimidines
1	simple plane for ribose and base rings covering area between ring bonds
2	simple plane for ribose and base rings covering area inside sticks (slightly smaller than mode 1)
3	plane bounded by sticks for ribose and base rings
4	large sphere of ring diameter at centre of ribose and each base ring
5	small sphere of 1/10 diameter at centre of ribose and each base ring

Examples

cartoon_ring_mode,0

cartoon_ring_mode,1

cartoon_ring_mode,2

cartoon_ring_mode,3

cartoon_ring_mode,4

cartoon_ring_mode,5

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

Cartoon ring finder

Settings

set cartoon_ring_finder, value

value	effect
0	no rings or sticks joining them
1	both ribose and base ring
2	only base ring(s), stick connects directly from phosphate to ring
3	very similar to ring finder 1, slight effect on transparency = distinct behaviour?
4	very similar to ring finder 1: finds ribose and base of nucleotides, and aromatic side chains of proteins
5	sticks visible but rings invisible

Examples

cartoon_ring_finder,0

cartoon_ring_finder,1

cartoon_ring_finder,2

cartoon_ring_finder,3

cartoon_ring_finder,4

cartoon_ring_finder,5

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

Cartoon ladder mode

Settings

set cartoon_ladder_mode, value

value	effect
0	no sticks shown
1	sticks show

Examples

cartoon_ladder_mode,0

cartoon_ladder_mode,1

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

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

Cartoon nucleic acid mode

Settings

set cartoon_nucleic_acid_mode, value

value	effect
0	smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain
1	smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain
2	smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on 5' end and O3' on 3' end (note takes O3' colour at terminus in default colouring)
3	appears same as mode 0?
4	appears same as mode 2? Seems to be what Pymol uses when it first opens nucleic acid containing file because any other settings change ends and colors.

Examples

cartoon_nucleic_acid_mode,0

cartoon_nucleic_acid_mode,1

cartoon_nucleic_acid_mode,2

cartoon_nucleic_acid_mode,3

cartoon_nucleic_acid_mode,4

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