The script file contains commands for MODELLER, in the TOP language (Chapter 4). A sample script file model-default.top to produce one model of sequence 1fdx from the known structure of 5fd1 and from the alignment between the two sequences is
# Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '5fd1' # codes of the templates SET SEQUENCE = '1fdx' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling
See Section 3.2 for information on the model script and its arguments.