The Chimera Window

The Chimera window includes a menu bar across the top. Optional features include a tool bar for extension icons, a line for status messages, and a command line (the Midas Emulator) across the bottom. The initial appearance of the window depends on any user startup files and predefined preferences.

Menu Bar

The bar across the top of the Chimera window contains pull-down menus for File, Select, Actions, Controllers, Settings, Extensions, and Help.

Tool Bar

The tool bar (optional, not shown) can contain icons for Chimera-associated programs or extensions. Tool bar display is set in the General preferences. Icons for extensions can be placed in the tool bar using the Extension Manager.

Graphics Window

Molecules, surfaces, and objects are displayed in the graphics window. The background color is black by default, and is controlled in the Background preferences.

Status Line

The display of a line for status messages (optional, not shown) can be controlled in the Messages preferences and the Accelerators dialog.

The Midas Emulator (Command Line)

Many commands used in MidasPlus (Chimera's predecessor) and several new commands can be entered into the Midas Emulator (see the commands index). The atom specification syntax is mainly the same, but there are some differences. Ctrl-u erases the contents of the command line. Past commands can be accessed using the Command History window.

The Midas Emulator can be opened by activating the checkbox next to Controllers... Midas Emulator. It is also an extension in the Keyboard category, and there are several ways to start an extension.

Besides allowing command entry, the Midas Emulator shows which models are open and active; the number of each open model is shown in bold, and the adjacent checkbox indicates whether the model is activated for motion (on by default). Clicking the box toggles between the activated and deactivated states. A deactivated model will not move in response to mouse manipulations in the main window or movement commands such as move and turn. The activation status of models can also be controlled in the Model Panel and with the command select.