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The ChimeraX Window

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:

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

Panels and Context Menus

A panel may appear within the ChimeraX window when a tool is started (for example, from the Tools menu or with the command toolshed show), or as the result of a calculation (for example, the interfaces command shows a chain-chain network diagram) or 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 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 panel can be:

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 Toolbar and Command Line lack title bars when docked, but the other methods of control are still available.

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.

Panels may have their own specific context menus (away from the title-bar area), typically including:

 ...and certain tool-specific preferences, when applicable:

Tool autostart behavior and dockability can also be set with the ui command.


UCSF Resource for Biocomputing, Visualization, and Informatics / July 2019