SET OUTPUT_CONTROL = 1 1 1 1 1
#READ_TOPOLOGY FILE = '$(LIB)/top.lib', TOPOLOGY_MODEL = 1
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib', TOPOLOGY_MODEL = 3
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = 'template'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = 'template', ALIGN_CODES = 'template'
SET SELECTION_SEARCH = 'SEGMENT', SELECTION_FROM   = 'ALL'
PICK_ATOMS SELECTION_SEGMENT =  '1'  '1',  SELECTION_STATUS = 'INITIALIZE'
PICK_ATOMS SELECTION_SEGMENT = '1'   '1',  SELECTION_STATUS = 'ADD'
#PICK_ATOMS SELECTION_SEGMENT = '7'   '7',  SELECTION_STATUS = 'ADD'
MUTATE_MODEL RESIDUE_TYPE = 'CSL'										# Mutate the selected residues into Cystein with spin label
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES 'MUTANT'   # Add the mutated sequence to the alignment arrays (it is now the second sequence in the alignment):
GENERATE_TOPOLOGY SEQUENCE = 'target'									# Generate molecular topology for the mutant:
TRANSFER_XYZ															# Transfer all the coordinates you can from the template native structure to the mutant 
																# (this works even if the order of atoms in the native PDB file is not standard):
BUILD_MODEL INITIALIZE_XYZ =off									        # Build the remaining unknown coordinates for the mutant:
WRITE_MODEL FILE = 'target.pdb'											# Write the mutant to a file: