# Homology modelling by the MODELLER TOP routine 'model'.
# Demonstrates how to refine only a part of the model.
#
# This can be ran with run_clustor model-loop.top, too.
#
# The difference with model-segment is that the loop is 
# refined on the basis of sequence alone, in the context
# of the rest of the structure.


INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1
SET SEQUENCE = 'TetraLoop'               # code of the target
SET LOOP_MODEL = 'Tetra.B99990001'   # initial model of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
# index of the first loop model:
SET LOOP_STARTING_MODEL = 1
# index of the last loop model:
SET LOOP_ENDING_MODEL = 10
SET LOOP_MD_LEVEL = 'refine_1'       # the loop refinement method (1 fast / 3 slow)

CALL ROUTINE = 'loop'

# This routine picks model residues that need to be refined (necessary):
SUBROUTINE ROUTINE = 'select_loop_atoms'
  # Uncomment if you also want to optimize the loop environment:
  # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6
  # A residue insertion (1st loop):
  PICK_ATOMS SELECTION_SEGMENT = '93:' '108:', SELECTION_STATUS = 'initialize'
  # B residue insertion (2nd loop):
  PICK_ATOMS SELECTION_SEGMENT = '300:' '315:', SELECTION_STATUS = 'add'
  # C residue insertion (3rd loop):
  PICK_ATOMS SELECTION_SEGMENT = '507:' '522:', SELECTION_STATUS = 'add'
  # D residue insertion (4th loop):
  PICK_ATOMS SELECTION_SEGMENT = '714:' '729:', SELECTION_STATUS = 'add'
  RETURN
END_SUBROUTINE

# This routine adds any special restraints (optional):
#
SUBROUTINE ROUTINE = 'special_restraints'
       MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '95:' '104:'
       MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '302:' '311:'
       MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '509:' '518:'
       MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '716:' '725:'
       SET RES_TYPES = 'ALL'
       SET ATOM_TYPES = 'ALL'
       SET SELECTION_STATUS = 'INITIALIZE'
       SET SELECTION_SEARCH = 'SEGMENT'
       SET SYMMETRY_WEIGHT = 0.5
       PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '93:' '108:'
       PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '300:' '315:'
       DEFINE_SYMMETRY ADD_SYMMETRY = on off
       PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '300:' '315:'
       PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '507:' '522:'
       DEFINE_SYMMETRY ADD_SYMMETRY = on off
       PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '507:' '522:'
       PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '714:' '729:'
       DEFINE_SYMMETRY ADD_SYMMETRY = on off
       PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '714:' '729:'
       PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '93:' '108:'
       DEFINE_SYMMETRY ADD_SYMMETRY = on off
   RETURN
END_SUBROUTINE