The __ model script implements the flowchart for comparative modeling by MODELLER that is described in the previous Section 3.1. The script uses routines in several other files. It is structured so that it is easy to deal with many different situations, some of which are described in Section 1.8. The script is too long to be listed here. It can be found in $MODINSTALL7v7/bin/__model.top. The default values of its arguments are defined in the __ defs script file:
# Define additional TOP variables needed for MODELLER:
DEFINE_INTEGER VARIABLES = STARTING_MODEL ENDING_MODEL RSTRS_REFINED
DEFINE_INTEGER VARIABLES = LOOP_STARTING_MODEL LOOP_ENDING_MODEL
DEFINE_INTEGER VARIABLES = MAX_ITERATIONS_STORE WRITE_INTERMEDIATES
DEFINE_INTEGER VARIABLES = IREPEAT REPEAT_OPTIMIZATION EXIT_STAGE
DEFINE_INTEGER VARIABLES = CREATE_RESTRAINTS REFINE_HOT_ONLY
DEFINE_INTEGER VARIABLES = MAX_VAR_ITERATIONS FINAL_MALIGN3D INITIAL_MALIGN3D
DEFINE_INTEGER VARIABLES = DO_LOOPS ID1B
DEFINE_REAL VARIABLES = VIOL_REP_STORE MAX_MOLPDF
DEFINE_REAL VARIABLES = MAX_CA-CA_DISTANCE MAX_N-O_DISTANCE
DEFINE_REAL VARIABLES = MAX_SC-SC_DISTANCE MAX_SC-MC_DISTANCE
DEFINE_STRING VARIABLES = MODEL MODEL2 CODE CODE2 ALNFILE MODEL2_FIT
DEFINE_STRING VARIABLES = CSRFILE KNOWNS SCHFILE FINAL_MODEL
DEFINE_STRING VARIABLES = GENERATE_METHOD RAND_METHOD MD_LEVEL
DEFINE_STRING VARIABLES = SEGFILE PDB_EXT TOPLIB PARLIB FAMILY FIT_IN_REFINE
DEFINE_STRING VARIABLES = ATOM_IDS1 ATOM_IDS2 OUTPUT2
DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL
DEFINE_STRING VARIABLES = LOOP_MD_LEVEL LOOP_INI_MODEL
DEFINE_STRING VARIABLES = LOOP_MODEL
DEFINE_STRING VARIABLES = TOP_VERSION
# For the academic version:
SET TOP_VERSION = 'academic'
# For the Accelrys version:
# SET TOP_VERSION = 'accelrys'
# read the residue types again, if the Accelrys lib required:
STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPERATION = 'ne', THEN = 'GO_TO __ACCELRYS7'
SET RESTYP_LIB_FILE = '$(LIB)/restyp_accelrys.lib'
READ_RESTYP_LIB
LABEL __ACCELRYS7
# default values for options in comparative modeling by MODELLER:
SET STARTING_MODEL= 1 # the index of the first model;
# determines how many models are calculated;
SET ENDING_MODEL = 1 # the index of the last model;
# determines how many models are calculated;
SET DEVIATION = 4.0 # the amount of randomization of the initial model
# must be > 0 if different final models are wanted;
SET DO_LOOPS = '0' # whether or not to do automatic loop refinement
# for each model *.B???????? (0 for no, 1 for yes)
# can rely on automatic loop definition or
# re-define select_loop_atoms routine.
SET LOOP_STARTING_MODEL = 1 # how many loop models to generate for
SET LOOP_ENDING_MODEL = 25 # each *.B????????
SET LOOP_MD_LEVEL = 'refine_3' # the same as for MD_LEVEL, but for loops
#
# Do not forget to set WATER_IO, HETATM_IO, HYDROGEN_IO to ON if your model
# includes WATER, HYDROGEN, and/or HETATM atoms.
#
# Additional flexibility is provided by re-defining the TOP routines
# 'select_atoms', 'special_restraints', 'special_patches', and
# 'rd_restraints'.
#
# Options that are not changed frequently:
SET LIBRARY_SCHEDULE = 4 # 1 ... thorough var target func schedule
# 4 ... faster var target func schedule
SET MAX_VAR_ITERATIONS = 200 # maximal numb of iterations for the cycles
# of the variable target function method
SET MD_LEVEL = 'refine_1' # what kind of optimization is done after
# the variable target function method:
# 'nothing' ... nothing;
# 'refine_1' ... very fast MD annealing;
# 'refine_2' ... fast MD annealing;
# 'refine_3' ... slow MD annealing;
# 'refine_4' ... very slow MD annealing;
# 'refine_5' ... very slow/large dt MD annealing;
SET REFINE_HOT_ONLY = 0 # 1 ... select and optimize only HOT atoms in refine;
# 0 ... select and optimize all atoms in refine;
# usually about half of the atoms are hot; in such cases,
# 0 is faster for sequences longer than about 100 aa
# because a faster non-bonded pairs algorithm can be used.
SET RSTRS_REFINED = 1 # the types of restraints used to define
# hot spots when MD_LEVEL <> 'nothing':
# 0 ... stereochemistry only;
# 1 ... stereochemistry and dihedral;
# 2 ... all restraints;
SET EXIT_STAGE = 0 # 0 ... no effect;
# 1 ... exit without any optimization after
# restraints and an initial model are
# calculated (more efficient than
# REPEAT_OPTIMIZATION=0);
# 2 ... exit after the initial model is calculated
# (restraints are not calculated)
SET REPEAT_OPTIMIZATION = 1 # how many times the whole optimization
# schedule (variable target function
# method and refinement) is repeated
# for each initial model;
SET TRACE_OUTPUT = 10 # every which CG or MD cycle is reported;
SET MAX_MOLPDF = 100E3 # abort optimization of the current model if
# the molecular pdf is larger than this and
# continue with the next model;
SET TOPLIB = '${LIB}/top_heav.lib' # topology library (all non-hydrogen atoms);
SET TOPOLOGY_MODEL = 3 # corresponding topology model;
SET PARLIB = '${LIB}/par.lib' # parameters library;
SET WRITE_INTERMEDIATES = 0 # 0 ... do not write out intermediate
# atom files during optimization;
# 1 ... write out intermediate atom files;
SET INITIAL_MALIGN3D = 0 # 0 ... do not do MALIGN3D before
# TRANSFER_XYZ
# 1 ... do that.
SET FINAL_MALIGN3D = 0 # 0 ... do not do MALIGN3D and write
# superposed templates & models
# at the end of 'model'
# 1 ... do that.
SET GENERATE_METHOD= 'transfer_xyz' # how to build the initial model:
# 'generate_xyz' from internal coordinates
# and write them to a file;
# 'transfer_xyz' from template coordinates
# and write them to a file;
# 'read_xyz' read coordinates from
# a file;
SET RAND_METHOD = 'randomize_xyz' # a method to perturb the initial model:
# 'randomize_dihedrals' ... uses DEVIATION
# in degrees;
# 'randomize_xyz' ... uses DEVIATION
# in angstroms;
# 'nothing'
SET CREATE_RESTRAINTS = 1 # 0 ... read the restraints from a file;
# 1 ... make the restraints and write them
# to a file before reading them
# for the optimization; in addition
# to the default restraints, the TOP
# routine 'special_restraints',
# which may be re-defined in the
# user TOP file, is called for any
# user defined restraints that are
# then also written to the same file.
SET SPLINE_ON_SITE = on # on ... convert some restraints into splines
# off ... no conversion
# SET OUTPUT_CONTROL = 1 1 1 1 0 # write real_output, notes, warnings, errors, dynmem
SET OUTPUT_CONTROL = 1 0 0 1 0 # write real_output, notes, warnings, errors, dynmem
# Set maximal values for various distance restraints:
SET MAX_CA-CA_DISTANCE = 14.0
SET MAX_N-O_DISTANCE = 11.0
SET MAX_SC-MC_DISTANCE = 5.5
SET MAX_SC-SC_DISTANCE = 5.0
# Routine 'user_after_single_model' can be redefined to do whatever at the end
# of each model calculation (e.g. comparison with X-ray structure).
# To write out reports on individual optimizations:
SET OUTPUT = 'NO_REPORT SHORT'
# The alignment file format (I/O):
SET ALIGNMENT_FORMAT = 'PIR'
# The extension added to all *.Bxxxxnn filenames:
SET PDB_EXT = '.pdb'
# to prevent SUPERPOSE in refine() if molecules are too small:
SET FIT_IN_REFINE = 'NO_FIT'
# To enable default filename generation if not explicitly defined:
SET MODEL = 'undefined'
SET CSRFILE = 'undefined'
# Call this routine before calling 'model' if you want real fast optimization
SUBROUTINE ROUTINE = 'very_fast'
# SET STARTING_MODEL = 1
# SET ENDING_MODEL = 1
SET MAX_CA-CA_DISTANCE = 10.0
SET MAX_N-O_DISTANCE = 6.0
SET MAX_SC-MC_DISTANCE = 5.0
SET MAX_SC-SC_DISTANCE = 4.5
# Note that all models will be the same if you do not change RAND_METHOD
SET RAND_METHOD = 'nothing'
SET MAX_VAR_ITERATIONS = 50
SET LIBRARY_SCHEDULE = 7
SET MD_LEVEL = 'nothing'
RETURN
END_SUBROUTINE