On a UNIX system, Chimera is started from the UNIX command line:
prompt> chimera [options] [input1 input2 ...]Bracketed arguments are optional. The user's execution path should include chimera_install_dir/bin (by default, chimera_install_dir is /usr/local/chimera).
On a Windows system, Chimera is started by clicking the chimera icon (a light-colored ring with a letter "C" hooked through it). To specify options or input files at startup, it is necessary to:
If a preferences file is found, it is also executed 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, Python commands 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 tool-specific type of file is opened, the associated tool will be executed or started, if it has not been started already.
Python is the default when no recognized prefix or suffix is supplied. If a prefix and an suffix are both given, the prefix overrides the suffix. Filenames, prefix and suffix types, and 4-character PDB identifiers are case-sensitive and (except for filenames) must be in lower case. Unrecognizable prefixes are assumed to be part of the filename.
If the input type is identified as PDB and the filename resembles a PDB identifier, but the file is not found in the working directory, Chimera will attempt to find it within a local installation of the Protein DataBank in /usr/mol/pdb/. If the file is not found locally, Chimera will then try to retrieve it from the Protein DataBank web site (by default; this can be turned off in the PDB preferences). If the input type is identified as SCOP, Chimera will try to retrieve the SCOP domain structure from the ASTRAL Compendium.
Files also can be read from within Chimera. One way is to use the command open; acceptable input types and rules for their specification are as described above, except that PDB format is the default. The other way is via open/save dialogs. For example, choosing File... Open from the menu brings up the main Chimera Open File Dialog.
Models can be closed with the command close, the Model Panel, or File... Close Session (which closes all open models).
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.