Cartoon representation

The cartoon representation of EasyHybrid is its own implementation: helices and strands are drawn as flat ribbons, with arrowheads on strands, and coils as round tubes. Secondary structure is assigned from the Cα trace with a P-SEA-like method, so no external program (such as DSSP) is needed. Breaks between chains and gaps in a chain are respected.

Showing the cartoon

• One object: right-click it in the tree and choose Representation > Cartoon.

• A whole system: right-click the system and choose Representation > Cartoon.

Clicking the cartoon selects the residue under the pointer.

Colors: Representation > Cartoon Setup...

• Secondary structure (default; the helix, strand and coil colors are set in Preferences);

• Rainbow (N- to C-terminus, per chain);

• Chain;

• Atom color (Cα);

• Single col

Fine tuning: Edit > Preferences > Viewer > Representations > Cartoon

• Ribbon dimensions: helix width and height, strand width and height, arrowhead width and taper (number of residues over which the arrowhead narrows), coil radius, ribbon detail (points per residue) and strand smoothing (straightens the pleated path of the strands).

• Secondary structure assignment: helix and strand tolerances (100% = published P-SEA thresholds; higher values classify more residues as helix or strand) and minimum helix and strand lengths. Dynamic secondary structure reassigns helices and strands on every frame of a trajectory; it is off by default, which is faster, and the cartoon still follows the coordinates.

• Colors: helix, strand and coil colors, and Transparency (%).