Cartoon Settings

  • cartoon_color (color, default:-1) controls the color of the cartoon representation.
  • cartoon_cylindrical_helices (boolean, default: off) controls whether helices are displayed as cylinders or as a residue-based cartoon.
  • cartoon_debug (integer: 0-3, default: 0) is for development.
  • cartoon_discrete_colors (boolean, default: off) affects whether per-residue colors change at or halfway inbetween the C-alpha position.
  • cartoon_dumbbell_length (float, default: 1.6) is a parameter for the dumbbell cross-section.
  • cartoon_dumbbell_radius (float, default: 0.16) is a parameter for the dumbbell cross-section.
  • cartoon_dumbbell_width (float, default: 0.17) is a parameter for the dumbbell cross-section.
  • cartoon_fancy_helices (boolean, default: off) controls whether dumbbell or oval cross-section is used.
  • cartoon_fancy_sheets (boolean, default: off) controls whether or not beta-sheet strands have arrows.
  • cartoon_flat_cycles (integer, default: 4) is the number of cycles of “flattening” applied to beta-sheets when cartoon_flat_sheets is on.
  • cartoon_flat_sheets (boolean, default: on) controls whether or not beta-sheet strands are flattened.
  • cartoon_helix_radius (float, default: 2.25) controls the radius of the cylindrical helix representation.
  • cartoon_highlight_color (color, default: -1) controls the accent color.
  • cartoon_ladder_color (color, default: -1) controls the color of the ladder representation.
  • cartoon_ladder_mode (integer, default: 1) controls how the ladder is drawn.
  • cartoon_ladder_radius (float, default: 0.25) controls the radius of the ladder representation.
  • cartoon_loop_cap (integer: 0-2, default: 1) controls how loop segments are capped:
    • 0 = not capped
    • 1 = round cap
    • 2 = flat cap
  • cartoon_loop_quality (integer, default: 6) controls how many facets are used to draw the loop cross-section.
  • cartoon_loop_radius (float, default: 0.2) controls the radius of loop segments.
  • cartoon_nucleic_acid_as_cylinders (boolean, default: on) controls whether or not PyMOL draws cartoon nucleic acids as high-quality cylinders or low-quality.
  • cartoon_nucleic_acid_color (color, default: -1) controls the control of nucleic acid backbone cartoons.
  • cartoon_nucleic_acid_mode (integer, default: 4) controls how the nucleic acid backbone is computed:
    • 0 = use P coordinates
    • 1 = use C1* coordinates
    • 2 = use P coordinates and terminal 3’ OH (if present)
    • 3 = use P coordinates and terminal 5’ OH (if present)
    • 4 = use P coordinates and both terminal 3’ and 5’ OHs (if present)
  • cartoon_oval_length (float, default: 1.35) is the length of the oval cross-section.
  • cartoon_oval_quality (integer, default: 10) controls how many facets are used to draw the oval cross-section.
  • cartoon_oval_width (float, default: 0.25) is the width of the oval cross section.
  • cartoon_power (float, default: 2.0) affects cartoon shape.
  • cartoon_power_b (float, default: 0.5) affects cartoon shape.
  • cartoon_putty_quality (float, default: 11) controls how many facets are used.
  • cartoon_putty_radius (float, default: 0.4) is the default putty size.
  • cartoon_putty_range (float, default: 2.0) is a putty scaling parameter.
  • cartoon_putty_scale_max (float, default: 4.0) is a putty scaling parameter.
  • cartoon_putty_scale_min (float, default: 0.6) is a putty scaling parameter.
  • cartoon_putty_scale_power (float, default: 1.5) is a putty scaling parameter.
  • cartoon_putty_transform (integer, default: 0) 0 is normalized nonlinear scaling; 1 is relative nonlinear scaling; 2 is scaled nonlinear scaling; 3 is absolute nonlinear scaling; 4 is normalized linear scaling; 5 is relative linear scaling; 6 is scaled linear scaling; 7 is absolute linear scaling from the B factor; and, 8 is implied RMS scaling.
  • cartoon_rect_length (float, default: 1.4) is the length of the rectangle cross-section.
  • cartoon_rect_width (float, default: 0.4) is the width of the rectangle cross-section.
  • cartoon_refine (integer, default: 5) controls how much refinement is done of intermediate cartoon coordinates.
  • cartoon_refine_normals (integer, default: -1) controls whether or not normals are refined (-1 = automatic).
  • cartoon_refine_tips (integer, default: 10) controls how much the tips of beta-strands are refined (straightened).
  • cartoon_ring_color (color, default: -1) controls the color of ring representation.
  • cartoon_ring_finder (integer, default: 1) controls how rings are detected:
    • 1 = all rings with a “C4*” or “C4” atom (e.g. nucleic acid bases)
    • 2 = all rings with a “C4” atom (e.g. carbohydrates)
    • 3 = all rings with a “C#” atom where # is any integer
    • 4 = all rings
  • cartoon_ring_mode (integer, default: 0) controls how rings are shown:
    • 0 = no ring (use ladders for bases, if applicable)
    • 1 = round-edge rings
    • 2 = square-edge rings
    • 3 = rings with edges
    • 4 = show ring as a sphere of approximate size
    • 5 = show ring centers as small spheres
  • cartoon_ring_radius (float, default: -1) controls the radius of the sphere used to represent rings (-1.0 means compute from ring geometry).
  • cartoon_ring_transparency (float, default: -1.0) controls the transparency level of rings. When negative, this setting is controlled by cartoon_transparency.
  • cartoon_ring_width (float, default: 0.125) controls the thickness of the ring representation.
  • cartoon_round_helices (boolean, default: on) controls whether or not PyMOL makes helices round by forcing orientation vectors to point along the helix axes.
  • cartoon_sampling (integer, default: 7) controls how many facets are used to draw cartoon segments.
  • cartoon_side_chain_helper (boolean, default: off) controls whether or not PyMOL will hide backbone lines and sticks when the cartoon representation is visible as well as disabling smoothing for C-alpha coordinates for residues whose side chains are shown.
  • cartoon_smooth_cycles (integer, default: 2) controls how many smoothing cycles are applied to the overall cartoon.
  • cartoon_smooth_first (integer, default: 1) controls the start point for smoothing each segment.
  • cartoon_smooth_last (integer, default: 1) controls the stop point for smoothing of each segment.
  • cartoon_smooth_loops (boolean, default: off) controls whether or not loop segments are smoothed. Note that this setting modifies the apparent coordinates of the loop in order to achieve improved aesthetics.
  • cartoon_throw (float, default: 1.35) affects cartoon geometry.
  • cartoon_trace_atoms (boolean, default: off) controls whether cartoons are traced through all atoms. Note that this setting only works well for the loop and tube representations.
  • cartoon_transparency (float, default: 0.0) controls the transparency of cartoon representations.
  • cartoon_tube_cap (integer, default: 2) controls the type of cap applied to the tube, and accepts the same values as cartoon_loop_cap.
  • cartoon_tube_quality (integer, default: 9) controls how many facets are used in the tube cross-section.
  • cartoon_tube_radius (float, default: 0.5) controls the radius of tube segments.
 
setting/cartoon.txt
 
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