The Chimera Window

Molecular structures and other 3D data are displayed in the graphics window. The background color can be changed:

• with the set command (for example, set bg_color white)
• with Actions... Color in the menu
• in the Background preferences
• by using a preset

• File
• Select
• Actions
• Presets
• Tools
• Favorites
• Help

The Chimera window may also include a toolbar for icons, a command line, and a status line. The initial appearance of the window depends on any startup files and predefined preferences.

The toolbar is only shown when it contains one or more icons, as specified in the Tools preferences. Toolbar location and orientation can be controlled in the General preferences.

When fullscreen mode (Windows only) is specified with the startup option --fullscreen or in the General preferences, the graphics window without borders will occupy an entire screen. The menu bar and any other components (tool bar, command line, and status line) can then be opened as a separate window with the F2 key, or just a pop-up menu can be used.

Command Line

Chimera commands are entered at the Command Line. There are several ways to start the Command Line, a tool in the General Controls category. Command targets are indicated with atom specification strings, which can include names, properties, zones, and combinations of these.

Ctrl-u erases the command line contents; the list of past commands can be traversed with up arrow and down arrow or Ctrl-p and Ctrl-n.

The black inverted triangle to the right of the command entry field marks a pulldown menu. The menu includes:

• the most recently entered commands
• Command History... for showing the full Command History; the total number of commands to remember (default 60) can be set in the Command Line preferences
• Hide Command Line (alternatively, the Command Line can be hidden using its instance in the bottom section of the Tools menu)

Below the command entry area, the number of each open model is shown in bold and a checkbox shows whether the model is activated for motion. Clicking the box toggles between the activated (default) and deactivated states. Checking All activates all open models. Model activation status can also be controlled in the Model Panel and with the command select.

Status Line

The display of a line for status messages can be controlled in the Messages preferences and the Keyboard Shortcuts dialog. Icons may be present and colored or grayed out depending on the situation:

• the red stop icon appears on the left when a foreground task is running; clicking it aborts the task
• the information icon is blue when one or more background tasks are running; clicking it, even when it is grayed out, brings up the Task Panel
• the magnifying glass icon is colored when something is selected; mousing over it reports in a text balloon what is selected, and clicking it brings up the Selection Inspector