Examples of nucleic acid cartoons
Revision as of 12:57, 9 December 2007 by Aflaus (talk | contribs) (Examples of cartoon ring and cartoon ladder settings moved to Examples of nucleic acid cartoons)
pymol version info
The various new nucleic acid display settings for PyMol 0.99 listed below were produced using version 0.99 beta 29 on Windows XP with an arbitrary B-form DNA molecule. Higher values could be set for each setting but appeared to yield the default representations.
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, 1 # backbone follows phosphates
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 as ring mode 0)
cartoon ring modes
set cartoon_ring_mode, 0 # no nucleotide rings
set cartoon_ring_mode, 1 # filled rings extending to outside edge of bonds
set cartoon_ring_mode, 2 # filled rings extending to inside edge of bonds
set cartoon_ring_mode, 3 # filled rings with bonds as thicker lines
cartoon ladder modes
set cartoon_ladder_mode, 0 # no ladder
set cartoon_ladder_mode, 1 # with ladder, as stick (if ring mode 0) or link to ring (if rings)
note that the visibility of the ladder sticks depends on ring mode >0, ring finder >0, nucleic acid mode = 0
all with: cartoon_ring_mode,3 cartoon_nucleic_acid_mode,0 cartoon_ring_finder,1
cartoon nucleic acid modes
set cartoon_nucleic_acid_mode, 0 # backbone follow phosphates (red)
set cartoon_nucleic_acid_mode, 1 # backbone follows C4' of ribose (green)
all with: cartoon_ladder_mode,0 cartoon_ring_mode,3 cartoon_ring_finder,1
cartoon ring finder
set cartoon_ring_finder, 0 # no ribose, base (or ladder)
set cartoon_ring_finder, 1 # ribose and base ring
set cartoon_ring_finder, 2 # base ring only
all with: cartoon_ladder_mode,1 cartoon_ring_mode,3 cartoon_nucleic_acid_mode,0