Open3DALIGN operations are controlled by a series of keywords, and their relative options. The syntax is very simple; the following example covers all possible cases:
keyword parameter_1=string_or_numeric_value_1 \
parameter_6="filename with spaces" \
parameter_7=filename\ with\ spaces
Keywords and parameters are separated by spaces or tabulations; no extra spaces should be inserted (e.g., between parameter and values or inside values) or error messages will be issued. Spaces can be inserted in values (e.g., for filenames containing spaces) only if the whole value is enclosed between quotes; alternatively, spaces can be preceded by a backslash (see example above). Comments can be entered after the
#symbol. Line feeds separate one keyword from the one which follows; as in the shell, one may divide parameters belonging to a single keyword by line feeds to improve readability of the scripts if a backslash is inserted before the line feed, as in the example reported above.
Here follows an alphabetic list of all currently available keywords. Clicking on each keyword an extended explanation will be provided along with all relevant options, examples of use and, when appropriate, details about the implementation and scientific background.