INCLUDE

SET ALNFILE     =       'as_meta1.modellerinput'
SET KNOWNS      =       '1DLP_sub' 
SET SEQUENCE    =       'as_meta1'
SET ATOM_FILES_DIRECTORY        =       '/home/daniel/lyase/model_construction'
SET STARTING_MODEL              =       1
SET ENDING_MODEL                =       10

SET HETATM_IO ON
SET RAND_SEED = -6482

SET DEVIATION     = 4

#####################################################################
# Change some of the defaults for more rigorous optimisation
#####################################################################

SET LIBRARY_SCHEDULE = 1      # 1 ... thorough var target func schedule
#SET LIBRARY_SCHEDULE = 4      # 1 ... thorough var target func schedule
                              # 4 ... faster var target func schedule
SET MAX_VAR_ITERATIONS = 400  # maximal numb of iterations for the cycles
#SET MAX_VAR_ITERATIONS = 200  # maximal numb of iterations for the cycles
#SET MAX_VAR_ITERATIONS = 50  # maximal numb of iterations for the cycles
                              # of the variable target function method

#SET MD_LEVEL = 'nothing'      # what kind of optimization is done after
SET MD_LEVEL = 'refine1'      # what kind of optimization is done after
#SET MD_LEVEL = 'refine3'      # what kind of optimization is done after
                              # the variable target function method:
                              # 'nothing'            ... nothing;
                              # 'refine1'            ... thorough MD annealing;
                              # 'refine2'            ... fast MD annealing;
                              # 'refine3'            ... very fast MD annealing;

#SET REPEAT_OPTIMIZATION = 2   # how many times the whole optimization
SET REPEAT_OPTIMIZATION = 1   # how many times the whole optimization
                              # schedule (variable target function
                              # method and refinement) is repeated
                              # for each initial model;

SET FINAL_MALIGN3D = 0              # 0 ... do not do MALIGN3D and write 
                                    #       superposed templates & models
                                    #       at the end of 'model'
                                    # 1 ... do that.
SET OUTPUT_CONTROL = 1 1 1 1        # write real_output, notes, warnings, errors

SET OUTPUT = 'REPORT LONG'
#SET OUTPUT = 'NO_REPORT SHORT'
#####################################################################
CALL ROUTINE = 'model'