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The ChimeraX window appears within a few seconds of startup in the default graphical user interface (GUI) mode. Depending on startup options and the Toolshed preferences, ChimeraX may connect to the Toolshed website to check for updates to installed bundles and for new features (commands, file formats) available from bundles that the user does not have installed. This connection occurs asynchronously, i.e., without slowing down the startup process or subsequent use of ChimeraX. See also: Startup preferences, Window preferences

On Windows,
ChimeraX can be started by clicking its icon. To specify options (stereo, nogui mode, etc.) or input files at startup, create a new shortcut:
  1. drag the ChimeraX icon with the right mouse button and select Copy Here from the menu to create another shortcut icon
  2. right-click the new icon, select Properties from the menu that appears
  3. in the resulting panel, click the Shortcut tab and then append the desired option(s) and input(s) to the command in the Target field. The path to the ChimeraX executable, arguments of options, and input file pathnames should be enclosed in quotation marks if they contain any spaces, for example:
    "C:\Program Files\ChimeraX\bin\chimerax.exe" --stereo --start "Side View"
  4. click the new icon to start ChimeraX with the specified options
On Linux,
ChimeraX can be started from the system command line:
$ chimerax [options] [input1 input2 ...]
... using the symbolic link to the executable created by the installer. (The executable is in the bin subdirectory of the ChimeraX installation.)
On Mac OS X,
ChimeraX can be started by clicking its icon or by drag-and-drop of known file types onto the icon. It can also be started from the Terminal command line:
$ chimerax_install_dir/Contents/MacOS/ChimeraX [options] [input1 input2 ...]
The chimera_install_dir is typically /Applications/ Starting from Terminal is one way to run multiple instances of the same ChimeraX installation on Mac.

Startup Input and Commands

Input files may contain data to be displayed or commands or code to be executed.

Any of the known file types can be opened from the system command line at the time of startup. The formats of files specified by local pathname or URL are indicated by filename suffixes. Files that are gzipped, as indicated by their additional .gz suffix, can also be read. Fetches from online databases are indicated by a source prefix followed by a colon, for example: emdb:1024
The default source prefix pdb: can be omitted if a valid 4-character identifier is supplied.

Python files in the directory ~/chimerax_start (where ~ is the user's home directory) are imported automatically at startup.

ChimeraX commands to execute at startup of the Command Line Interface can be specified in the Startup preferences. If ChimeraX is started in nogui mode without command/script file input, a prompt will be supplied in the system shell for entering commands on standard input.

Exit from ChimeraX

ChimeraX can be exited by clicking to dismiss the window, using the ChimeraX menu to Quit, or by entering exit or quit in the Command Line.

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