Examples of nucleic acid cartoons

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Contents

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

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