Chimera Startup

On Windows,
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).
On Mac OS X,
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 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.

Startup Files

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

System Command-Line Input

Input files may contain structures to be displayed, commands or code to be executed, or other data. If Chimera is started in nogui mode without command/script file input, a prompt will be supplied in the system shell for entering Chimera commands on standard input.

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. For many of the registered file types, files that are gzipped (as indicated by .gz following the regular filename) are recognized and opened. Similarly, compressed files (*.Z) can be recognized and opened for many input types if gzip is on the user's execution path (can be run by entering gzip at 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.

Input within Chimera

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

In addition, many tools bring up dialogs to open specific file types.

On a Mac, dragging and dropping known file types on the Chimera icon will start Chimera (if not already started) and open the files.

Models can be closed with the command close, the Model Panel, or File... Close Session.

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.

UCSF Computer Graphics Laboratory / November 2008