READ_MODEL FILE='TEMPLATE'
SEQUENCE_TO_ALI ATOM_FILES = 'TEMPLATE', ALIGN_CODES = 'TEMPLATE'

READ_MODEL FILE='u'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'u', ALIGN_CODES = ALIGN_CODES 'u'

MALIGN

READ_MODEL FILE='TEMPLATE'
READ_MODEL2 FILE='u'

# The trick of reading the files once more is needed, because there is a bug that makes MODEL2 inaccessible for the SEQUENCE_TO_ALI command.


# WRITE_ALIGNMENT FILE='ble.ali'
# Pick and superpose all atoms within 6 A of the CA atom in Cysteine 88

PICK_ATOMS ATOM_TYPES='ALL', SPHERE_RADIUS= 10.0, ;
	 SELECTION_SEARCH = 'SPHERE', SPHERE_CENTER = '88:' 'CA'
SUPERPOSE

WRITE_MODEL2 FILE='tmp.pdb' 