# Homology modelling by the MODELLER TOP routine 'model'.
# Demonstrates how to refine only a part of the model.
#
# You may want to use the more exhaustive "loop" modeling routines instead.
#

INCLUDE                             # Include the predefined TOP routines

SET ALNFILE  = '/home/people/RET/ret4p.ali'      # alignment filename
SET KNOWNS   = '/home/peolpe/RET/1AI1sp.pdb'               # codes of the templates
SET SEQUENCE = '/home/people/RET/ret4'               # code of the target
SET ATOM_FILES_DIRECTORY = '/home/people/RET' # directories for input atom files
CHECK_ALIGNMENT
SET STARTING_MODEL= 1               # index of the first model 
SET ENDING_MODEL  = 1               # index of the last model
                                    # (determines how many models to calculate)
#SET DYNAMIC_FLAG = 0                # selected atoms do not feel the neighbourhood
SET MD_LEVEL = 'refine1'

CALL ROUTINE = 'model'              # do homology modelling


#SUBROUTINE ROUTINE = 'select_atoms'
#  PICK_ATOMS SELECTION_SEGMENT='36:' '38:', SELECTION_SEARCH='segment', ;
#             PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ;
#             SELECTION_FROM='all', SELECTION_STATUS='initialize', SELECTION_STEP=1
#  RETURN
#END_SUBROUTINE