Cartoon

Added in version 3.17.0.

This visual element renders the cartoon representation of a protein structure: alpha helices are drawn as flat ribbons, beta strands as ribbons ending in an arrow head that indicates the chain direction, and all other parts of the polymer backbone (coil) as thin tubes. The visual element is automatically attached to the cartoon data object created by the PDB and mmCIF file readers.

To combine the cartoon with an atomistic representation of, for example, the side chains or ligands only, use the Expression selection modifier together with the Cartoon Flags particle property that the file readers attach to the atoms. See the cartoon data object page for details.


Cartoon representation of PDB entry 27EM, colored by secondary structure type.	Close-up of the same structure: the cartoon combined with a ball-and-stick representation of a ligand.

Parameters

Coloring

Selects how the residues are colored. In Secondary structure mode, each residue is colored according to its secondary structure type (helix, strand, coil). The colors of the three types can be changed in the Types tab of the data inspector or in the pipeline editor under the cartoon data object. In Chain mode, residues are colored according to the polymer chain they belong to. In Uniform mode, the entire cartoon is rendered in a single color.

If the cartoon object has a Color property, e.g. assigned by the Color coding modifier, the per-residue colors take precedence over the selected coloring mode.

Helix width

The width of the ribbons representing alpha helices. Default: 2.0.

Strand width

The width of the ribbons representing beta strands. Default: 2.0.

Arrow head width

The maximum width of the arrow heads terminating beta strands. Default: 3.5.

Ribbon thickness

The thickness of the ribbons representing helices and strands. Default: 0.25.

Coil radius

The radius of the tubes representing coil regions. Default: 0.25.

Quality

Controls the visual quaility of the cartoon visualization. The backbone spline is sampled adaptively: straight stretches receive few samples, while strongly curved or twisted regions such as helices receive more. Higher quality levels produce smoother ribbons and rounder coil tubes at higher compuational cost.

In the default Automatic mode, the level is chosen based on the number of residues of the structure, such that the performance remains high even for very large assemblies: High up to 5,000 residues, Medium up to 20,000, Low up to 50,000, and Lowest beyond that.

Strand arrow heads

Controls whether beta strands are terminated with an arrow head.

Hint

The cartoon follows the atoms it is built from. To wrap the cartoon into a periodic simulation cell, wrap the atoms with the Wrap at periodic boundaries modifier. The visual element then cuts the ribbons and tubes at the cell boundaries.