Chimera can be started by clicking the chimera icon. To specify options or input files at startup:

1. drag the chimera icon with the right mouse button and select Copy Here from the menu that appears; this creates another shortcut icon called "copy of chimera"
2. right-click the new copy of chimera 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 Chimera executable, arguments of options, and input file pathnames should each be enclosed in double quotes if they contain any spaces, for example:

   "C:\Program Files\Chimera\bin\chimera.exe" --stereo "f:\PDB Files\protease.pdb"
   

4. click the the new copy of chimera icon

Chimera can be started from the system command line:

> chimera [options] [input1 input2 ...]

Bracketed arguments are optional. The user's execution path should include chimera_install_dir/bin (the default chimera_install_dir is /usr/local/chimera).

Chimera can be started by clicking the chimera icon or by dragging and dropping certain file types on the chimera icon. The drag-and-drop approach currently works for the Chimera web data (*.chimerax) and PDB (*.pdb) file types.

Chimera can also be started from the system command line:

> chimera_install_dir/Contents/MacOS/chimera [options] [input1 input2 ...]

Bracketed arguments are optional. The default chimera_install_dir is /Applications/Chimera.app.

Chimera for Mac OS X (X Windows) requires an X server to be installed and running. Starting this version of Chimera will automatically start the X server if it is not already running.

If a Chimera preferences file is found, it is read at startup. If a midasrc file is found (see the Midas preferences), it will be executed when the Command Line is shown.

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

Any of the registered file types can be opened from the system command line at the time of Chimera startup. File type can be specified by a suffix that is part of the filename or by prefix:filename, where prefix is not part of the filename. If a prefix and a suffix are both given, the prefix overrides the suffix. Filenames, prefixes, and suffixes are case-sensitive. Unrecognizable prefixes are assumed to be part of the filename. Files that are gzipped (as indicated by .gz following the regular filename) are recognized and opened. Python is the default type of input from the system command line.

Input is generally specified as a pathname to a file or the name of a file in the current working directory. In some cases (indicated with certain prefixes), the filename can be the database identifier of a file to be retrieved and opened. Internet connectivity is required to fetch files over the Web.

Any of the registered file types can also be opened from within Chimera. The most general ways are:

• with File... Open (local files), Fetch by ID (files to be fetched from databases)
• from the Chimera Command Line, using the command open (default type PDB)

On a Mac, dragging and dropping certain file types on the Chimera icon will open them in a running instance of Chimera that was previously started by clicking the icon. The drag-and-drop approach currently works for the Chimera web data (*.chimerax) and PDB (*.pdb) file types.

Models can be closed with the command close, the Model Panel, or File... Close Session (which closes all open models).

Exit from Chimera

A Chimera session can be terminated by choosing File... Quit from the menu, or by entering the command stop in the Command Line. By default, the user is asked to confirm exit, but this can be turned off in the General preferences.