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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 additional options 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. See also: --script
--debug
Activate debugging mode.
--exit
Exit ChimeraX after executing the rest of the command (applying other options and reading input); do not access the Toolshed.
--lineprofile
Create a “ChimeraX.lprof” file in the current directory for line profiling.
--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
Create a buffer for offscreen rendering in nogui mode.
--script  python-script [ arguments ]
Run the specified python script with any associated arguments after starting tools. See also: --cmd
--silent
Skip the splash screen and otherwise refrain from being verbose.
--start  tool_name
Start the specified tool after the autostarted tools.
--stereo
Start in sequential stereo if the hardware permits. See also: camera
--uninstall
Deregister any icons or mime types, and then remove as much of the installation directory as possible.
--usedefaults
Ignore user settings and use factory defaults.

Line Profiling

Line profiling is based on Robert Kern's line_profiler package. There are five parts to profiling; differences from the conventional setup are given in parentheses:

  1. Decorate functions that you wish to profile with the “@line_profile” decorator (instead of the conventional “@profile”) and install them. This decorator is a no-op if ChimeraX is not profiled.
  2. Run ChimeraX with the --lineprofile option (instead of using “kernprof”) to generate a “ChimeraX.lprof” file in the current directory.
  3. Get profiling results by running ChimeraX with the system command-line option “-m line_profiler ChimeraX.lprof” (not described above)
  4. Analyze the results, possibly edit your code, and return to step 1.
  5. Remove the function decorators before committing your changes.

See the ChimeraX Programming Manual for more details.


UCSF Resource for Biocomputing, Visualization, and Informatics / July 2018