Overview
Pymol has a complex group of settings for controlling the way nucleic acids are represented, broadly separated into:
- ring, for ribose and base ring(s)
- ladder, for the sticks connecting the backbone, ribose and base ring(s)
- nucleic acid, for the smooth backbone path
Each setting can be altered with the set command. The cartoon settings affect each other so experimentation may be necessary to achieve what you want. Many of the mode settings only seem to work at the global level and cannot be applied to individual objects or selections.
Ring settings
Ring mode
Ring mode defines the representation of the ribose and base.
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
|
| 6+ |
appears to default to ring mode 2
|
Ring finder
Ring finder defines the rings which are recognised
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, slight effect on transparency = distinct behaviour?
|
| 5 |
sticks visible but rings invisible
|
| 6+ |
appears to default to ring finder 5
|
Other settings for ring
set cartoon_ring_xxx, value
| xxx |
value |
effect
|
| color |
color |
set the colour of the ring or sphere
|
| width |
float |
thickness of ring for planes and sticks (modes 1, 2, 3)
|
| radius |
float |
radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring in mode 4, approx 1/10 ring diameter in mode 5
|
| transparency |
float |
transparency of ring or sphere, does not affect sticks in ring mode 3
|
Ladder settings
Ladder mode
Ladder mode affects the sticks connecting the backbone to ribose and ribose to base, and ring mode 0 or ring finder 5.
set cartoon_ladder_mode, value
| value |
effect
|
| 0 |
no sticks shown
|
| 1 |
sticks show
|
| 2+ |
appears to default to ladder mode 1
|
Other settings for ladder
set cartoon_ladder_xxx, value
| xxx |
value |
effect
|
| color |
color |
colour of the stick
|
| radius |
float |
stick width for ring modes 1, 4 and 5 (default is 0.25), in other ring modes the ladder stick width is controlled by the ring width instead
|
Nucleic acid settings
Nucleic acid mode
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.
|
| 5+ |
appears to defult to nucleic acid mode 0
|
Note
Note that in ring mode 0 or ring finder 2 the stick projects from the backbone at a point midway between phosphates
set ribbon_nucleic_acid_mode, value
| xxx |
value |
effect
|
| ribbon_nucleic_acid_mode |
integer |
has the equivalent behaviour to cartoon_nucleic_acid_mode
|
Other settings for nucleic acid
set cartoon_nucleic_acid_xxx, value
| xxx |
value |
effect
|
| color |
color |
backbone colour (default is backbone atom colour)
|
Third-party Wrappers
- dssr_block can create "block" shaped base pair cartoons with DSSR