Difference between revisions of "Overview of nucleic acid cartoons"

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(New page: == 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 s...)
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Revision as of 12:48, 9 December 2007

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, for example:

set cartoon_ring_mode, 1

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.

cartoon_ring_mode 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

cartoon_ring_finder 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 rin
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 rings

cartoon_ring_color color set the colour of the ring or sphere
cartoon_ring_width float thickness of ring for planes and sticks (modes 1, 2, 3)
cartoon_ring_radius float radius of ring for spheres (modes 4, 5), negative number gives sphere of same radius as ring for mode 4, approx 1/10 ring diameter mode 5
cartoon_ring_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.

cartoon_ladder_mode 0 no sticks shown cartoon_ladder_mode 1 sticks shown cartoon_ladder_mode 2+ appears to default to ladder mode 1

Other settings for ladder

cartoon_ladder_color color colour of the stick cartoon_ladder_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

cartoon_nucleic_acid_mode 0 smooth backbone passing through phosphorus atoms, backbone terminates at last phosphorus on either end of chain cartoon_nucleic_acid_mode 1 smooth backbone passing through ribose C3' atoms, backbone terminates at last C3' on either end of chain cartoon_nucleic_acid_mode 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) cartoon_nucleic_acid_mode 3 appears same as mode 0? cartoon_nucleic_acid_mode 4 appears same as mode 2? cartoon_nucleic_acid_mode 5+ appears to defult to nucleic acid mode 0 ribbon_nucleic_acid_mode has the equivalent behaviour to cartoon_nucleic_acid_mode

Other settings for nucleic acid

cartoon_nucleic_acid_color color backbone colour (default is backbone atom colour)