Main Window Shortcut Menus

Selection shortcut menu
Workspace shortcut menu
Bond shortcut menu
Sequence viewer shortcut menu
Related Topics

Several of the main window components have shortcut menus, which you open by right-clicking and holding over the component. The shortcut menus for the status bar and the command input area only have two items, Hide, which hides the component, and Help, which displays the relevant help topic. In addition to Hide and Help, the toolbar shortcut menu has Customize, to customize the choice of icons on the toolbar, and Style, which provides a choice of icon, text, or both for the buttons on the toolbar.

The Workspace has three shortcut menus: one for the Workspace itself (the Workspace shortcut menu), one for the atoms in the current selection (the selection shortcut menu), and one for bonds (the bond shortcut menu). The selection shortcut menu is also available from the sequence viewer, but has a more limited selection of items, and has a few additional items. The items on these menus are described below. Where relevant, conditions on when the item is displayed are included.

When you right-click and hold in the Workspace:

On an unselected atom, the atom becomes the selection and the selection shortcut menu is displayed.
On a selected atom, the selection shortcut menu is displayed.
On a bond, the two atoms in the bond are selected and the bond shortcut menu is displayed.
On empty space, if there is an atom selection, the selection shortcut menu is displayed, otherwise the Workspace shortcut menu is displayed.

The sequence viewer shortcut menu can be uses to perform various actions on the sequences or the display. If you do not have any residues selected in the sequence viewer, the sequence viewer shortcut menu is displayed. If you have residues selected, the selection shortcut menu is displayed.

Selection shortcut menu items.
Menu Item		Action
Apply Zoom to All Tiles		Apply the zoom value from the current tile to all tiles. Only available in tile mode from the Workspace.
Apply View to All Tiles		Apply the view (rotation, translation, zoom) from the current tile to all tiles. Only available in tile mode from the Workspace.
Reset Tile		Reset the view of the current tile to its initial value. Only available in tile mode from the Workspace.
Pick Tiles to Move		Turn on or off picking to move tiles. When enabled, picking selects tiles which can then be moved to a new location. Only available in tile mode from the Workspace.
Background Color		Set the Workspace background color to black, white, gray, or blue.
Workspace Feedback		Set up entry properties to be shown at the top left of the Workspace ("feedback"). Opens the Preferences panel at the Feedback – Entry section.
Invert Selection		Select the unselected atoms and deselect the selected atoms.
Expand Selection		Expand the selection to include atoms within a specified distance of the current selection. Submenu that includes items for the distance, including a Custom item for setting the distance; an option to exclude the current selection (so that the atoms within the distance become the selection); and an option to include all atoms in residues that have atoms within the specified distance (Expand Residues). Only available from the Workspace.
Select Matching Atoms by		Select all atoms that match any of the currently selected atoms, by Color, Representation, or Element (which you choose from the submenu). For example, if the selection has red and green atoms and you choose to select by color, all red and green atoms are selected. Only available from the Workspace.
Representation		Set the molecular representation to wire frame, ball and stick, CPK, tube, or thin tube.
Color Scheme		Apply the color scheme from the submenu to the selected atoms. If this menu is opened from the sequence viewer, there is an extra color scheme, 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.
Labels		Apply the label from the submenu to the selected atoms.
Highlights		Add a highlight of a particular type with the default settings or manage highlights. Only available from the Workspace.
Display		Display the entire molecule or residue containing the selected atoms. This action is useful if part of the molecule or residue was previously undisplayed. Display residues with atoms within a chosen distance of the selected atoms.
Display Only		Display only the selected atoms, or the selected atoms plus residues that have atoms within a chosen distance of the selected atoms. Only available from the Workspace.
Undisplay		Undisplay the selected atoms.
Delete		Delete the selected atoms.
Switch Alternate Positions		For atoms with partial occupancy, switch between the alternate positions. Only available from the Workspace.
Display Alternate Positions		For atoms with partial occupancy, display all positions. The alternate positions are displayed as ghosts. Only available from the Workspace.
Set Element		Change the selected atoms to atoms of the element chosen from the submenu. The submenu contains a selection of common elements, and an Other item for selecting other elements from a periodic table. Only available from the Workspace.
Insert Gap		Insert a gap in the sequence to the left of the first selected residue. Opens a dialog box in which you can specify the size if the gap, in residues. Only available from the sequence viewer.
Mutate Residue		Change the residues that contain the selected atoms (or the selected residues) to the type chosen from the submenu.
Rotamers		Open the Rotamers dialog box to select one of the standard rotamers for the selected residues.
Create Project Entry		Create a project entry. Opens the Create Entry from Selected Atoms dialog box, in which you can provide a title for the entry, and choose whether to create the entry from all atoms, the selected atoms, or the displayed atoms. Only available from the Workspace.
Exclude Entries		Exclude the entries that contain the selected atoms from the Workspace.
Select Project Entries		Select the entries that contain the selected atoms in the Project Table. The submenu allows you to choose whether to add the entries to the current Project Table selection, or to replace the selection. The Project Table and Entry List scroll to the last of these entries.
Fit to Workspace		Fit the displayed structure to the Workspace and reset the center of rotation.
Clip		Clip the display to the selected atoms (moves the clipping planes). Only available from the Workspace.
Center Electron Density		Center the displayed electron density map on the centroid of the selected atoms. Only available from the Workspace.
Transform		Perform a local transformation. Only available from the Workspace.
Align Centers of Mass		Translate the structures to align the centers of mass of the selected atoms in each entry. Only available from the Workspace.
Help		Open this help topic.

Workspace shortcut menu items.
Menu Item		Action
Apply Zoom to All Tiles		Apply the zoom value from the current tile to all tiles. Only available in tile mode.
Apply View to All Tiles		Apply the view (rotation, translation, zoom) from the current tile to all tiles. Only available in tile mode.
Reset Tile		Reset the view of the current tile to its initial value. Only available in tile mode.
Background Color		Set the Workspace background color to black, white, gray, or blue.
Workspace Feedback		Set up entry properties to be shown at the top left of the Workspace ("feedback"). Opens the Preferences panel at the Feedback – Entry section.
Save Image		Open the Save Image panel to save an image of the Workspace in TIFF, JPEG, or PNG format.
Save View		Save the current view of the Workspace (orientation, location, and zoom).
Restore View		Restore the last saved view of the Workspace (orientation, location, and zoom).
Manage Views		Open the Manage Views panel to work with the saved Workspace views.
Fit to Workspace		Fit the displayed structure to the Workspace and reset the center of rotation.
Create Entry from Workspace		Create a Project Table entry from the Workspace.
Clear Workspace		Clear the Workspace.
Delete		Delete labels, measurements, or adjustments.
Highlights		Add or change highlights on the Workspace structures.
Caption		Add captions to the Workspace, delete captions or edit captions.

Bond shortcut menu items.
Menu Item		Action
Order		Set the bond order to zero, one, two, or three.
Measure		Measure the bond length and display it. The measurement is added to the list in the Measurements panel.
Adjust		Adjust the bond length or the dihedral angle around this bond.
Delete		Delete the bond.

Sequence viewer shortcut menu items.
Menu Item		Action
Hide		Hides the sequence viewer. To redisplay it, use the View menu.
Color Scheme		Colors the sequence with the scheme selected from the submenu. The choices are: None, Color by Chain, Alpha Carbon, Residue Charge, Residue Position, Residue Type, Residue Property, Secondary Structure, Template ID, and Color Breaks.
Font Size		Sets the font size for the sequence viewer. Choose Small, Medium, Large, or Huge from the submenu.
View SSA		Shows or hides the secondary structure assignment for the sequence.
Display Non-protein Molecules		Display non-protein molecules in the sequence viewer. Three lines are used, for ligands, waters, and ions.
Show Displayed Residues Only		Shows only the residues that are displayed in the Workspace.
Align by Residue Number		Aligns the sequences in the sequence viewer by residue number. (Does not affect the alignment of the structures.) This command enables gaps to be displayed in the sequence viewer.
Exclude Entry		Excludes the entry containing this chain from the Workspace. The chain is removed from the sequence viewer. If the entry contains multiple chains, all the chains in the entry are removed from the sequence viewer.
Wrap Sequences		Wraps the sequence display so that long sequences are displayed across multiple lines with vertical scrolling rather than on a single line with horizontal scrolling.
Legend		Opens the Sequence Viewer Legend dialog box, which explains the sequence color schemes.
Preferences		Opens the Sequence Viewer - Preferences dialog box, in which you can set the proximity cutoff.
Save Image		Opens the Save Sequence Viewer Image file selector, in which you can select an image format and save an image of the sequence viewer to a file.
Export Sequences		Exports the sequences in the Sequence Viewer to a FASTA file. Opens a file selector to specify the location and the file name.
Help		Displays the Sequence Viewer help topic.

Main Window Shortcut Menus

Related Topics