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System Command-Line Options

The following options are available when ChimeraX is invoked from the system command line. Arguments containing spaces should be enclosed in quotation marks, and input files can be given after the options. Not all options are listed here; see the ChimeraX Programming Manual for the full list of options, including several that may be relevant to developers.

Some of the options give information about ChimeraX without starting it:

--help
List all system command-line options.
--listioformats
List the known file types along with their filename suffixes and whether each type can be opened and/or saved.
--version
Report program version. If given twice, list the versions of all installed ChimeraX tools. If given three times, list the versions of all installed Python packages.

Most of the options control behaviors upon ChimeraX startup:

--cmd  command
Run the specified ChimeraX command after starting tools. Do not check the Toolshed website for updates, regardless of the frequency of checking specified in the Toolshed preferences. See also: --script
--exit
Exit ChimeraX after executing the rest of the command (applying other options and reading input). Do not check the Toolshed website for updates, regardless of the frequency of checking specified in the Toolshed preferences. The converse option --noexit also specifies skipping the Toolshed check, but not automatically exiting from ChimeraX.
--nocolor
In nogui mode, do not colorize text output. Otherwise, messages to standard output are colored as follows: info green, warning yellow, error red, status magenta, prompt bright blue. If --nocolor is used, message type is instead indicated with a prefix in capital letters, for example: STATUS: Exiting ...
--nogui
Do not show the graphical user interface. See also: --nocolor, --offscreen
--nostatus
Do not send messages to the status line.
--notools
Do not autostart any tools.
--offscreen
Use nogui mode and create a buffer for offscreen rendering. This option enables “headless” mode, allowing ChimeraX to render and save images and movies when it has no window, e.g., on a server where no desktop windowing system is available. It is currently supported only on Linux and uses OSMesa, a software rendering library included in Linux ChimeraX. It cannot use a graphics card or hardware-accelerated rendering because OpenGL does not support rendering without a window.
--script  python-script [ arguments ]
Run the specified python script with any associated arguments after starting tools. Do not check the Toolshed website for updates, regardless of the frequency of checking specified in the Toolshed preferences. See also: --cmd
--start  tool_name
Start the specified tool after the autostarted tools.
--stereo
Start in sequential stereo if the hardware permits. See also: camera
Not yet implemented:
--usedefaults
Ignore user settings and use factory defaults.

UCSF Resource for Biocomputing, Visualization, and Informatics / June 2021