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The syntax of commands is described using the following rules: Capitalized words are keywords that must be specified as is. However, if the word is partially capitalized, it may be abbreviated to the capitalized part. Lower case words are to be replaced by a corresponding data entry. The symbol `::=' means "has the following syntactic form:". Anything enclosed in square brackets, `[]', is optional. If several things are stacked in square brackets, one may choose one optionally. Anything enclosed in curly brackets, `{}', specifies that a selection must be made of the choices stacked vertically inside. The syntactic entities which appear as an argument to `repeat' may be repeated any number (including zero) times. Defaults for optional parameters may be enclosed in apostrophes and placed under the entity they stand for. However, defaults are not specified in this manner if the rules for the default are complex.
The syntactic glossary, see Syntactic Glossary, contains further syntactic entities which are used in the command descriptions. Finally, the options and operands in each command can usually be specified in any order except if otherwise noted.
As an illustration of the syntax notation, the plot command in the analysis facility has following syntax:
PLOT [titspec] [HORIZ real real integer]
titspec ::= TITLE string del
Assuming the standard definition of the del, a syntactically acceptable command is
PLOT HORIZ 1.0 10.3 60 TITLE BOND ENERGY PER RESIDUE $