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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)
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
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
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
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
