MODELLER is run by
mod script_file_namewhere script_file_name is the name of the script file with instructions for MODELLER. This file contains commands in the TOP language. Each command line consist of the name of the command and optional variable assignments that control the action of the command. The scope of the variables is global; that is, once a variable is assigned on any command line, the assigned value remains in effect, in the main program and all subroutines, until explicitly changed by another assignment or, in a few cases, by MODELLER. All the commands and the default values of the variables are listed in Section 5.4. This Chapter describes the TOP commands that are used for dealing with proteins; the general TOP commands (e.g., assignment, flow control, arithmetic operations) are described in Chapter 4.
See directory examples for examples of the TOP scripts that use commands described in this Chapter. In particular, sub-directory examples/commands contains the examples used in this Chapter. Another set of TOP scripts that you could use as templates can be found in the scripts directory.