GARLIC CONFIGURATION FILE, TEMPLATE RESIDUES AND DOCUMENTATION
Garlic will try to open two files at startup: the system-wide configuration file (.garlicrc) and PDB file with template residues (residues.pdb). Garlic documentation package may be added to /usr/share/doc directory or some HTML directory or to some HTML directory.
(1) CONFIGURATION FILE:
Up to seven attempts to open the configuration file will be made. Only the first available file is used. If all seven attempts fail, default parameters will be used. Default parameters are hard-coded in the file read_config.c.
File name: .garlicrc (or garlicrc, but only for one directory!). C source file: open_config_file.c ---------------------------------------------------------------------------- (1.1) ./.garlicrc (the current working directory) (1.2) $HOME/.garlicrc (the home directory, $HOME or $home) (1.3) $HOME/garlic/.garlicrc (1.4) /usr/share/garlic/.garlicrc (recommended as system-wide default!) (1.5) /etc/garlicrc (note that file name is garlicrc !)
(1.6) /usr/local/lib/garlic/.garlicrc
(1.7) /usr/lib/garlic/.garlicrc
(2) TEMPLATE RESIDUES (building blocks for proteins etc.): Up to six (6) attempts to open the file with template residues will be made. Only the first available file is used. If not available at all, the template residues will not be available. The commands CREATE and REPLACE will be useless, but the program will work (with limited capabilities).
File name: residues.pdb C source file: open_template_file.c ---------------------------------------------------------------------------- (1.1) ./residues.pdb (the current working directory) (1.2) $HOME/residues.pdb (the home directory, $HOME or $home)
(1.3) $HOME/garlic/residues.pdb
(1.4) /usr/share/garlic/residues.pdb (recommended as system-wide default!)
(1.5) /usr/local/lib/garlic/residues.pdb
(1.6) /usr/lib/garlic/residues.pdb
RESUME:
The suggested pathnames (see below) should be useful for most Linux and Unix distributions. If you accept these paths and pathnames, please note that the configuration file should be called .garlicrc and not garlicrc! Both files (.garlicrc and residues.pdb) may be found in the original source package. If you don't like the suggestions, please edit open_config_file.c and/or open_template_file.c !
System-wide configuration file: /usr/share/garlic/.garlicrc System-wide file with template residues: /usr/share/garlic/residues.pdb
Garlic documentation directory: /usr/share/doc/garlic/ or
/var/www/html/garlic/ or
some_other_html_directory !