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Command: cartoon, ribbon

Usage:
cartoon | ribbon )  atom-spec  [ smooth  factor | default ] [ suppressBackboneDisplay  true | false ]

Usage:
cartoon hide | ribbon hide )  atom-spec 

The cartoon or ribbon command shows a simplified backbone representation of the specified biopolymer residues. The command cartoon hide (ribbon hide) hides cartoon for the specified residues. The commands hide and show can also be used to control cartoon display. Protein secondary structure (helix and strand) assignments are read from the input structure file or calculated with dssp. See also: rungs, struts, Molecule Display Toolbar

Cartoon settings are only changed when explicitly specified; there are no command defaults, only initial default settings of a structure when it is first opened. Changes only apply to models that are already present, not those opened later.

The following settings can be different for different residues:

smooth  factor
The factor controls the balance between smoothing peptide β-strands versus following the exact positions of the α-carbons (initial default 1.0 maximally smoothed, ranging to 0.0 for unsmoothed). Specifying default instead of a numerical value sets the value to 1.0. Smoothing applies only to peptide strands, not to helices, coil, or nucleic acids. Lower values may be desired for strand residues with sidechains displayed, to preclude showing tethers.
suppressBackboneDisplay  true | false
Whether showing cartoon for a residue suppresses the display of its backbone atoms (initial default true). The backbone atoms suppressed by cartoons are N, C, and O in amino acids and the phosphate moieties including O5' in nucleic acids. Simultaneous display can be enabled by setting this option to false.

The subcommands of cartoon, however, control per-model settings:

The cartoon path is guided by CA atoms (α-carbons) in peptides and C5' in nucleic acids. The transverse orientation of a residue's ribbon segment is set according to the type of secondary structure and/or polymer:

Peptide residues at the beginning or end of a secondary structure element (SSE) are given the same orientation as the adjacent residue in that SSE. The depiction of a peptide helix or strand starts at the CA atom of its first (N-terminal) residue and ends at the CA atom of its last (C-terminal) residue.

Cartoon Subcommands: Style, Tether

The subcommands cartoon style and cartoon tether control per-model settings.

cartoon | ribbon ) style  atom-spec  [ width  w ] [ thickness  t ] [ xsection  oval | rectangle | barbell ]  model-options 

The cartoon style command controls secondary structure representations, width, thickness, and shape. Given without options, it reports the current settings for each atomic model.

The following options can have different values for helix, strand, coil, and/or nucleic in the same model (and these words can be used in the atom-spec). Conversely, a blank atom-spec indicates all applicable models and secondary structure types.

The width w and thickness t are given in Å. The width setting does not affect coil, however, as only its thickness is used in both dimensions. The initial default width and thickness are 2.0 and 0.4 Å, respectively.

The xsection or cross-sectional shape of the cartoon can be oval (synonym round), rectangle (synonym square), or barbell with rounded edges and a thinner middle (synonym piping). The barbell cross-section does not apply to coil and does not affect arrowheads. The initial default cross-section is oval for helix and coil, rectangle for strand and nucleic.

The following cartoon style model-options have only a single value per model:

modeHelix  tube | wrap | default
The modeHelix option allows showing peptide helices as tubes (curved cylinders) rather than as ribbons spiraling along the backbone atoms (initial default). Spiraling ribbons from the wrap mode wrap around the calculated tubes, whereas those from the initial default mode are oriented as described above.

Helix tube calculations use α-carbon coordinates. For a helix of 6 or more residues, a straight tube axis (first principal component) is used if it gives a low average distance to the α-carbons; otherwise, an arc (circle segment) fit to the α-carbon coordinates is used instead. For a helix of 3-5 residues, the axis of an idealized α-helix fit to the α-carbons is used. Increasing the number of sides from 12 is recommended to give tubes a more rounded (smoother) appearance. Other than radius and sides, most helix settings such as width, height, cross-section, and arrows do not apply to helices in the tube mode. Tube-helix example:

cartoon style  modeh tube  rad 2.0  sides 24
radius  r | auto
For peptide helices in the tube mode only, a constant radius r can be specified, otherwise (auto, default) a radius will be determined separately for each helix according to the average distance of the α-carbons to the tube midline, capped at a maximum of 2.5 Å. Where a displayed α-carbon is offset from the tube surface, a tether will be drawn.
sides  N
The number of straight-line segments used to draw an oval cross-section or the circumference of a tube, with higher numbers corresponding to finer subdivisions (initial default 12). Shading is used to give a smooth, rounded appearance despite this approximation of the shape. See also: graphics
arrows  true | false
Whether to show arrowheads at the C-terminal ends of peptide strands (initial default true).
arrowsHelix  true | false
Whether to show arrowheads at the C-terminal ends of peptide helices (initial default false).
arrowScale  factor
The factor (initial default 2.0) is multiplied by the width of helix or strand to give the arrowhead width.
divisions  N
The number of divisions per residue along the path of the ribbon (initial default 20). See also: graphics
barSides  Nb
The number of straight-line segments used to draw a barbell cross-section (initial default 18). Odd values of barSides Nb are automatically rounded up to the next even number.
barScale  factor
The factor (range 0.2–1.0, initial default 0.5) is multiplied by the thickness to give the central “bar” thickness of barbell cross-section relative to the edges, where the nominal value applies.

More examples:

cartoon style width 1.5 thick 0.3
cartoon style helix width 1.5 thick 0.3
car style strand xsection rect width 2
cartoon style nucleic width 2 thickness 2 xsection round
rib style x rect
rib style (#1 & coil) x round
cartoon style #2 arrows f wid 1 thick 1 x round
cartoon | ribbon ) tether  atom-spec  [ shape cone | steeple | cylinder ] [ sides  Nt ] [ scale  scale ] [ opacity  opacity ]

The command cartoon tether controls the appearance of the connectors between α-carbons and the cartoon where they are offset. Such offsets may be visible where sidechains are displayed on smoothed strands or helix tubes. A tether is drawn between a displayed α-carbon (CA atom) and the corresponding cartoon segment where they are offset. Tether shape can be:

The sides option controls the number of planar facets used to draw a tether (range 3-10, initial default 4). The scale option sets tether base radius relative to the display radius of the corresponding α-carbon (range 0.0-1.0, initial default 1.0). The tether opacity value (1 – transparency) can range from 0.0 (completely transparent, allows hiding the tethers) to 1.0 (completely opaque), with initial default 0.5. The tether color tracks the color of the corresponding α-carbon.

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2017