Overview of nucleic acid cartoons

From PyMOLWiki
Jump to: navigation, search

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