Sequence Viewer

The sequence viewer displays the sequence of the proteins that are included in the Workspace. Each chain is displayed on a separate line. The left column of the sequence viewer lists the entry name for the sequence, with the chain name appended. The right column displays the actual sequence as a list of single-letter codes, and also displays the secondary structure assignment, if one is available. If the protein contains ligands, waters, or ions, these are displayed in separate "sequences", one for each type of molecule. (These molecules are identified by the corresponding ASL expressions.)

To show or hide the sequence viewer, you can:

• Choose Window → Sequence Viewer in the main window.

The background colors of the sequences reflect the current coloring scheme for the alpha carbon in the Workspace. Each residue in the sequence also has a tooltip that gives the residue name, number, and insertion code.

If the protein has a secondary structure assignment, the assignment is displayed above the sequence, using the following symbols:

• Helices are displayed as tubes, colored red
• Strands are displayed as arrows, colored cyan
• Loops are displayed as a gray line

You can select residues in the sequence and perform actions on these residues.

• To select a single residue, click the residue.
• To add single residues to the selection or remove single residues from the selection, control-click the residues.
• To select a range of residues, either click the first and shift-click the last, or drag over the residues. If the sequence viewer is wrapped, you can drag over multiple rows to select residues in more than one row; the residues that are selected are those in the sequence in which you started dragging.
• To change the selection of a range of residues to the selection, hold down CTRL and drag over the residues.The unselected residues are selected, and the selected residues are deselected.

The selected residues are highlighted in reverse video (as colored letters on a black background), and are marked in yellow in the Workspace. You can also select the missing residue locations in gaps.

You can zoom in on a single residue by middle-clicking on it. This action does not select the residue, but spot-centers on the alpha carbon and fits the residue to the screen. If you middle-click on a gap, the structure is not spot-centered but the view is zoomed in to the residues on either side of the gap.

The sequence viewer and the Workspace are synchronized: selection of atoms in the Workspace selects the corresponding residues in the sequence viewer, and selection of residues in the sequence viewer selects them in the Workspace. Likewise, changing the color scheme in the Workspace changes the color scheme in the sequence viewer, and vice versa. Structural changes, such as mutating a residue, are also reflected in the sequence viewer.

To zoom in on a residue in the Workspace without selecting it, middle-click the residue in the sequence viewer.

The sequence viewer has a shortcut menu (right-click and hold), which you can use to perform various actions on the sequences or the display. The sequence viewer shortcut menu is displayed when you right-click in the left pane of the sequence viewer, or when you right-click in the right pane of the sequence viewer when there are no residues selected. The menu items are described in the Main Workspace Shortcut Menus topic.

If you have residues selected, a version of the Workspace shortcut menu is displayed, with the following changes:

• Switch Alternate Positions, Display Alternate Positions, Clip, Center Electron Density, and Transform are not present.

• Set Element is replaced by Insert Gap, which opens a dialog box that allows you to specify the number of residues in the gap. The gap is inserted to the left of the selected residue. To delete residues from a gap, select the residues and choose Delete from the shortcut menu.

• There is one extra item on the Color Scheme submenu: Proximity. If you choose this item, the residues within a given distance of the selected residues are colored orange, and the selected residues are colored red. All others are colored gray. The distance is specified in the Sequence Viewer - Preferences dialog box, which you open from the sequence viewer shortcut menu.