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Tool: Command Line Interface

ChimeraX commands are entered at the Command Line Interface. This interface can be opened from the Tools menu (more...). See also: help, usage, ChimeraX window, command usage conventions

Sometimes it is necessary to click in the graphics window or command line to take back focus from some other dialog so that command keystrokes will register. When the focus is in the command line or graphics window, the history can be navigated and commands edited as described below.

Dragging and dropping the icon for a file or directory into the command line substitutes the corresponding pathname text.

The inverted triangle to the right of the command line marks a pulldown menu. The menu includes:

Whether to Leave Failed Command Highlighted (so that typing another command will automatically erase it) is a preference that can be set using the command-line context menu. The initial default is to leave a failed command unhighlighted in the command line so that it can be edited rather than erased.

Command History

Previously used commands are remembered in the Command History. The commands can be re-executed and/or saved to a file. Whether the history should show Typed Commands Only is a preference that can be set using the context menu in the command line or history panel. Typed commands are those explicitly entered by the user rather than generated automatically by clicking toolbar icons, using the File History to open data, etc. The number of commands to remember (initial default 500) is also a preference; it includes all commands, of which the typed commands are only a subset. See also: Log

The Command History panel can be opened from the pulldown menu marked by a triangle or chevron to the right of the Command Line Interface.

In the Command History panel, double-clicking an individual command executes that command. Individual commands or blocks of commands may be chosen (highlighted) using the left mouse button. Ctrl-click adds to an existing choice rather than replacing it. To choose a block of commands without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block. Some of the buttons act only upon the chosen command(s):

The command history can also be navigated directly in the command line regardless of whether the Command History panel is shown. With the focus in the command line or graphics window:

Navigation skips commands for which the entire line is identical. When the mouse focus is in the command line (not the graphics window), another way to navigate the history is with the keyboard up arrow and down arrow, alone or in combination with Shift (meaning previous/next use of the same command, as described above for Ctrl-p/n). The arrow keys also work to navigate the command history when the mouse focus is in the graphics window but nothing is selected.

The history is stored in a file in a platform-dependent standard location and carries over between different ChimeraX sessions. The location can be reported with command:

info path user unversioned data

UCSF Resource for Biocomputing, Visualization, and Informatics / August 2020