Chimera Startup

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

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. Input file names must include path information and should be enclosed in double quotes if they contain any spaces, for example:
   "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 chimerax (*.chimerax) and PDB (*.pdb) file types. The X server must already be running for for Mac-X11 versions of Chimera to start. Chimera can also be started from the system command line, using the executable:

> chimera_install_dir/Contents/MacOS/chimera

(the default chimera_install_dir is /Applications/Chimera.app). Options and input files can be specified at the command line, as shown above for UNIX.

If a preferences file is found, it is read upon Chimera startup. Preferences, including the location of the preferences file, are set within the Preferences preferences. If a midasrc file is found, the commands within it are executed if (or when) the Command Line is shown; the file is treated as if it had been sourced. The locations of any midasrc files are set in the Midas preferences.

Input files may contain structures to be displayed, commands or code to be executed, or other data; Chimera can read any input types that have been registered. The type of a file whose name is entered at the system command line can be specified by a suffix that is part of the filename or by prefix:filename (where the prefix is not part of the filename). If a prefix and an suffix are both given, the prefix overrides the suffix. Unrecognizable prefixes are assumed to be part of the filename. Python is the default when no recognized prefix or suffix is supplied.

Files that are gzipped (as indicated by .gz following the regular filename) are recognized and opened. If a tool-specific type of file is opened, the associated tool will be executed or started, if it has not been started already.

In some cases, the "filename" can be the database identifier of a file to be retrieved and opened. If the input type is identified as PDB and the filename resembles a PDB identifier, the corresponding file will be retrieved from the Protein Data Bank, as described for Fetch by ID. The prefix ndb: indicates an NDB identifier and the prefix scop: indicates a SCOP domain identifier; in either case, the file will be retrieved from the appropriate database as described for Fetch by ID.

Filenames, prefix and suffix types, and 4-character PDB identifiers are case-sensitive and (except for filenames) must be in lower case.

Any of the registered file types can also be opened from within Chimera. The most general ways to open a file are with the Chimera Open File Dialog, the Fetch by ID dialog, and the command open. In addition, many tools bring up dialogs to open specific file types.

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 chimerax (*.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 after File... Quit has been chosen; this can be turned off in the General preferences.