The ChimeraX Window

ChimeraX has an all-in-one window interface in which various panels can be shown, hidden, and repositioned. Panels can also be detached (undocked) from the main ChimeraX window and subsequently reinserted (docked).

The overall window also contains the main window for 3D graphics, a title bar at the top, and a status line for transient messages across the bottom. By default, a Toolbar with icons lies right below the title bar. Near the bottom right corner are additional small icons:

• or – toggle main window to fill overall window (see also ui windowfill)
• or – toggle main window between 3D graphics and Rapid Access
  (see File History)

See also: camera, windowsize, mousemode, Window preferences, ChimeraX menu

Panels and Window Controls
Hiding and Cycling Through Windows
Context Menus
Using ChimeraX Fullscreen

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Panels and Window Controls

A panel may appear within the ChimeraX window:

• when a tool is started (for example, from the Tools menu or with the command tool show)
• as the result of a calculation (for example, the interfaces command shows a chain-chain network diagram)
• as the result of opening a certain type of data (for example, opening a density map starts Volume Viewer)

Panels may include clickable icons, interactive 2D representations like network diagrams, and (rendered) HTML with links and images, as in the Help Viewer. Users can define custom panels of buttons with the buttonpanel command. A panel can be:

• dismissed by clicking the “x” button on its title bar (if the panel is docked; a generic close-window button if the panel is undocked) or by unchecking its name in the context menu of any docked panel's title bar
• shown (if active but hidden) by checking its name in the bottom section of the Tools menu or in the context menu of any docked panel's title bar; some panels remain active when dismissed, others do not
• undocked from the main ChimeraX window by clicking the “rectangles” button on its title bar or by dragging or double-clicking its title bar; tools without a title bar (the Toolbar and Command Line) have a context menu option to Undock
• if dockable, redocked by dragging or double-clicking its title bar, with the dragged location controlling where and how the panel will be inserted
• tabbed with other panels when dropped in the same area; tabs are shown at the bottom of the tabbed set, and clicking a tab brings the corresponding panel to the front

The overall window or any undocked panel can be resized by dragging any corner and moved by dragging its title bar. The boundaries between docked panels or between panel(s) and the main window can be dragged to expand one side and shrink the other while keeping the overall window dimensions the same.

The overall window can be toggled to hide/show the current panels by clicking the “nested squares” button near its bottom right corner. This allows expanding the main window with a single click without losing the overall window configuration. The Toolbar and Command Line are excluded from this toggling.

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Hiding and Cycling Through Windows

A single running instance of ChimeraX may have multiple windows, namely the main window (including all of its docked panels) plus any panels that are undocked or “floating.” Keyboard Shift-Esc can be used to hide/show all of the undocked panels collectively, as if using the command ui hideFloating toggle.

Platform-specific hotkeys cycle through the set of ChimeraX windows, bringing each in turn to the front. See the hotkey assignments listed for a platform as NextChild (cycle windows in a certain order) and PreviousChild (cycle windows in the opposite order) in the Qt standard shortcuts table.

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Context Menus

A context menu is raised by right-clicking* parts of the interface. See also: selection context menus, Right Mouse icons

*for Mac trackpad or single-button mouse, Ctrl-click replaces “right-click” for showing context menus

A general context menu can be accessed from the title bar of any docked panel. In addition, panels may have their own specific context menus (away from the title-bar area), typically including:

• Hide Tool
• Help – show documentation in the Help Viewer

• Start at ChimeraX Startup – whether the tool should start automatically upon subsequent ChimeraX startup
• In Favorites Menu – whether the tool should be listed in the Favorites menu
• Dockable Tool – whether panels of the tool should be allowed to reinsert automatically when dragged over the main window, as opposed to remaining separate; initially true for most panels, with exceptions including Help Viewer and Settings (Preferences)
• Save Tool Position – save whether a tool panel is docked, and if so, whether it is on the left, right, top, or bottom side of the main window (but not the specific order when multiple panels are docked on the same side); save tabbing, if saved for each tool in a tabbed set; if undocked, save panel size and screen position

Tool preferences can also be set with the ui command.

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Using ChimeraX Fullscreen

To use ChimeraX graphics fullscreen with controls on a separate screen:

• the Command Line and icon Toolbar can be undocked from the graphics window by choosing Undock from their respective context menus, then dragged to the other display
• other tool panels can also be dragged to the other display, or closed, or hidden collectively using the icon in the status line (bottom right)
• command ui statusbar false hides the status line
• command ui fullscreen true makes the ChimeraX window fill the screen and hides its title bar
• command ui menubar false hides the menus (on Windows)