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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 across the top, and a status line for transient messages across the bottom. At the bottom right are 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 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

*for Mac touchpad 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.

Toolbars and the Command Line lack their own title bars, but the other methods of control are still available. An icon toolbar can be grabbed for repositioning by clicking the small dashed line on its top or left end, and dragged to the left, right, top, or bottom side of the main window. Disclosing icons that would extend beyond the toolbar requires either enlarging the overall window or clicking the double arrowhead to show an additional row or column of icons. On some systems, the double arrowhead does not show the icons properly except in Rapid Access mode, which can be toggled on and off as described above.

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. Toolbars and the 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 / March 2019