Ribbon Style Editor

Barstar (1bta) ribbon with Chimera default scaling in the style named aitch

Ribbon Style Editor allows ribbon scalings, styles, and residue classes to be edited directly and/or named and saved for subsequent use.

Secondary structure ribbons for peptides, proteins, and nucleic acids can be displayed using the command ribbon or the Actions menu. Which style of ribbon is shown can be controlled with the command ribrepr or the Actions menu.

There are several ways to start Ribbon Style Editor, a tool in the Graphics category. It has three panels shown as index cards:

• Scaling
• Cross Section
• Residue Class

SCALING

The scaling of a ribbon is its secondary-structure-specific height and width.

In the Scaling panel of the Ribbon Style Editor, changes can be entered directly, or the arrows on either side of a field can be clicked to increase or decrease the value by 0.05-angstrom increments. Only values greater than zero are allowed. Changes will not take effect until either Apply or OK is clicked; OK also dismisses the panel. Restrict OK/Apply... allows the scaling to be applied to only the current selection.

If a ribbon were to be laid out on a flat surface, the Width is the dimension parallel to the surface but perpendicular to the long axis of the ribbon, and the Height is the dimension perpendicular to the surface. Height settings only affect styles with a thickness (the built-in flat style is only affected by changes in Width).

Nucleic acid structures are shown with the Nucleic ribbon. For proteins, Helix and Sheet segments are as defined by HELIX and SHEET records in the input file or by ksdssp; the remainder is shown as Turn. Strands (the Sheet segments) are shown by default as arrows pointing in the C-terminal direction. Setting the Arrow (tip) and Arrow (base) widths the same as the Sheet width turns off the arrow appearance. Setting the Arrow tip and base widths equal to the Turn width also turns off the arrow appearance but shortens the strand somewhat. Setting all the widths equally small generates a simple spaghetti-like representation.

The settings in the Scaling panel collectively define a scaling, which can be named, saved, and later retrieved from the pulldown list indicated by the solid black triangle next to the Ribbon Scaling field. When the name Chimera default is shown, it is only possible to save to a different name, using Save As.... When another name is shown, it is possible to:

• Save the scaling to the name shown
• use Save As... to save the scaling to a new name
• Delete the scaling whose name is shown (if previously saved)

Custom style "aitch"

CROSS SECTION

The style of a ribbon is defined by its cross section (general shape perpendicular to the long axis) and how the cross section is smoothed.

In the Cross Section panel of the Ribbon Style Editor, a cross-section can be defined by placing points on a grid. The Number of grid divisions can be adjusted as needed for the complexity of the desired cross-section. A ribbon with a particular cross-section is subject to whichever scaling is in effect. The extent of the grid X-axis equals the width and the extent of the grid Y-axis equals the height. Using the built-in styles as examples:

• the edged (sharp) style corresponds to a square outlining the grid; when width differs from height, the cross-section is "squashed" to a rectangle
• the flat (ribbon) style corresponds to a horizontal line bisecting the grid; only the width matters, as this style has no height
• the round (rounded, smooth) style corresponds to the largest circle that fits in the grid; when width differs from height, the cross-section is "squashed" to an oval

A style is further defined by Display Options:

• Closed cross section - close the cross section automatically as it is being drawn on the grid (a line will connect the first and last points drawn); unnecessary if the closing line is created manually
• Smooth across ribbon - slightly round the corners of the cross section when drawing the ribbon
• Smooth along ribbon - generate a ribbon that flows smoothly from one residue to another (as opposed to a ribbon with obvious residue segmentation)

The settings in the Cross Section panel collectively define a style, which can be named, saved, and later retrieved from the pulldown list indicated by the solid black triangle next to the Ribbon Cross Section field. When the name of a built-in style is shown, it is only possible to save to a different name, using Save As.... When another name is shown, it is possible to:

• Save the style to the name shown
• use Save As... to save the style to a new name
• Delete the style whose name is shown (if previously saved)

RESIDUE CLASS

A ribbon residue class is defined by which atoms control the path of the ribbon and which atoms are considered part of the backbone (mainchain atoms). The path of the ribbon is controlled by two atoms per residue: the guide atom sets ribbon location (the path is smoothed over five successive residues), and the orientation atom sets the plane of the ribbon. By default, when ribbon is shown, mainchain atoms are:

• hidden, unless bonded to non-mainchain atoms or to atoms in residues not shown as ribbon
• adjusted to fall on the ribbon

The Residue Class panel of the Ribbon Style Editor allows new ribbon residue classes to be defined. Names for the Guide atom, Orientation atom, and Mainchain Atoms must be supplied. A mainchain atom's Position is how far along a residue's ribbon segment the atom is placed when adjusted to fall on the ribbon (possible values range from 0 to 1). Clicking Set adds the contents of the Name and Position fields to the Mainchain Atoms list. Choosing (clicking) an entry in the list and then clicking Remove deletes that entry.

Further Options:

• Non-helix/sheet uses "Nucleic" scaling - whether the ribbon for residues without secondary structure assignments should have the Nucleic dimensions in the current scaling scheme (otherwise the Turn dimensions will be used)
• Rotate orientation 90 degrees - whether the plane of the ribbon should be perpendicular to a line drawn from the middle (widthwise) of the ribbon to the orientation atom (otherwise parallel)

The settings in the Residue Class panel collectively define a ribbon residue class, which can be named, saved, and later retrieved from the pulldown list indicated by the solid black triangle next to the Ribbon Residue Class field. When the name of one of the built-in classes is shown, it is only possible to save to a different name, using Save As.... When another name is shown, it is possible to:

• Save the class to the name shown
• use Save As... to save the class to a new name
• Delete the class whose name is shown (if previously saved)