The top.ini file contains the list of all MODELLER commands, arguments, and default values of arguments.
--- COMMANDS:
1 no_action
2 SET
3 STOP
4 LABEL
5 GO_TO
6 DEFINE_INTEGER
7 DEFINE_REAL
8 END_DO
9 DO
10 CALL
11 RESET
12 WRITE
13 OPERATE
14 STRING_OPERATE
15 DEFINE_STRING
16 DEFINE_LOGICAL
17 SUBROUTINE
18 END_SUBROUTINE
19 INCLUDE
20 RETURN
21 READ
22 OPEN
23 CLOSE
24 IF
25 WRITE_TOP
26 SYSTEM
27 INQUIRE
28 STRING_IF
31 READ_RESTRAINTS
32 READ_SCHEDULE
33 WRITE_RESTRAINTS
34 READ_MODEL
35 SUPERPOSE
36 COMPARE
37 WRITE_MODEL
38 WRITE_MODEL2
39 OPTIMIZE
40 ENERGY
41 READ_MODEL2
42 PICK_ATOMS
43 ROTATE_DIHEDRALS
44 READ_ALIGNMENT
45 DELETE_ALIGNMENT
46 SWITCH_TRACE
47 PATCH
48 TRANSFER_RES_NUMB
49 MAKE_SCHEDULE
50 WRITE_SCHEDULE
51 ID_TABLE
52 MAKE_WRITE_UHBD_LIB
53 BUILD_MODEL
54 GENERATE_TOPOLOGY
55 MAKE_RESTRAINTS
56 READ_TOPOLOGY
57 READ_PARAMETERS
58 WRITE_TOPOLOGY_MODEL
59 MAKE_TOPOLOGY_MODEL
60 ROTATE_MODEL
61 WRITE_ALIGNMENT
62 REORDER_ATOMS
63 PICK_RESTRAINTS
64 CONDENSE_RESTRAINTS
65 DELETE_RESTRAINT
66 ADD_RESTRAINT
67 TRANSFER_XYZ
68 RANDOMIZE_XYZ
69 DEBUG_FUNCTION
70 undefined70
71 PICK_HOT_ATOMS
72 REINDEX_RESTRAINTS
73 ALIGN
74 SEQUENCE_SEARCH
75 ALIGN3D
76 ORIENT_MODEL
77 DESCRIBE
78 SEQUENCE_COMPARISON
79 MALIGN3D
80 MALIGN
81 SEQUENCE_TO_ALI
82 PMF
83 MUTATE_MODEL
84 PATCH_SS_MODEL
85 WRITE_DATA
86 PRINCIPAL_COMPONENTS
87 READ_ALIGNMENT2
88 COMPARE_ALIGNMENTS
89 ALIGN_CONSENSUS
90 QUICK_AND_DIRTY
91 SPLINE_RESTRAINTS
92 RENAME_SEGMENTS
93 DEFINE_SYMMETRY
94 PATCH_SS_TEMPLATES
95 CHECK_ALIGNMENT
96 ALIGN2D
97 COLOR_ALN_MODEL
98 IUPAC_MODEL
99 DENDROGRAM
100 EXPAND_ALIGNMENT
101 UNBUILD_MODEL
102 READ_ATOM_CLASSES
103 SEGMENT_MATCHING
104 READ_RESTYP_LIB
105 WRITE_PDB_XREF
106 MAKE_REGION
--- KEYWORDS:
1 REAL ARGUMENTS 0 0.00 # real arguments to the math operation
31 REAL UPDATE_DYNAMIC 1 0.39 # when to update non-bonded pairs list
32 REAL MATRIX_OFFSET 1 0.00 # substitution matrix offset for local alignment
33 REAL SPHERE_STDV 1 0.05 # standard deviation of soft-sphere repulsion
34 REAL VIOL_REPORT_CUT 33 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 4.5 999 999 999 999 4.5 4.5 4.5 4.5 4.5 4.5 999 6.5 4.5 4.5 4.5 4.5 4.5 999 999 999 # cutoffs for reporting relative violations
35 REAL DEBUG_FUNCTION_CUTOFF 3 0.01 0.001 0.1 # cutoffs for reporting differences between numerical and analytical derivatives: absolute, relative errors, factor_for_indiv_rstrs
36 REAL TRANSLATION 3 0.0 0.0 0.0 # translation vector for MODEL
37 REAL SA_STEP 1 0.2 # amplitude of the Monte Carlo steps
38 REAL SA_MVFRACT 1 0.8 # fraction of accepted Monte Carlo steps
39 REAL SA_TFACTR 1 0.9 # factor for temperature deacrease in MC SA
40 REAL SA_T0 1 40.0 # starting SA temperature
41 REAL SA_TMIN 1 0.01 # final SA temperature
42 REAL MIN_ATOM_SHIFT 1 0.010 # minimal atomic shift for the optimization convergence test
43 REAL DEVIATION 1 0.0 # coordinate randomizaton amplitude in angstroms
44 REAL RMS_CUTOFFS 11 3.5 3.5 60 60 15 60 60 60 60 60 60 # cutoffs for RMS, DRMS, Alpha Phi Psi Omega chi1 chi2 chi3 chi4 chi5
45 REAL TEMPERATURE 1 293.0 # temperature for MD simulation in K
46 REAL MD_TIME_STEP 1 4.0 # time step for MD in fs
47 REAL RADII_FACTOR 1 0.82 # factor for van der Waals radii
48 REAL LENNARD_JONES_SWITCH 2 6.5 7.5 # the range for Lennard-Jones interaction smoothing to 0
49 REAL COULOMB_SWITCH 2 6.5 7.5 # the range for Coulomb interaction smoothing to 0
50 REAL ROTATION_MATRIX 9 1 0 0 0 1 0 0 0 1 # rotation matrix for MODEL
51 REAL BASIS_RELATIVE_WEIGHT 1 0.05 # the cutoff weight of basis pdf's for their removal
52 REAL SYMMETRY_WEIGHT 1 1.0 # the weight of the symmetry objective function term
53 REAL MAXIMAL_DISTANCE 1 999. # maximal distance for distance restraints
54 REAL RESTRAINTS_FILTER 33 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 -999 # keep restraints?
55 REAL RESTRAINT_PARAMETERS 0 3 1 3 3 4 2 0 0.0 0.087 # restraint parameters
56 REAL SPHERE_RADIUS 1 10.0 # sphere radius for atoms selection
57 REAL SELECTION_SLAB 5 -9999 9999 0 0 0 # slab for atoms selection: \Z{dz1} \Z{dz2} \Z{xtrans} \Z{ytrans} \Z{ztrans}
58 REAL PICK_HOT_CUTOFF 1 4.0 # radius for picking hot atoms
59 REAL CAP_ATOM_SHIFT 1 0.2 # limit for atomic shifts in optimization
60 REAL MOLPDF 1 0.0 # value of objective function
61 REAL GAP_PENALTIES_3D 2 0.0 1.75 # gap creation and extension penalties for structure/structure superposition
62 REAL CONTACT_SHELL 1 4.0 # distance cutoff for calculation of the non-bonded pairs list
63 REAL RESTRAINT_STDEV 2 0.0 1.0 # transforming factors for standard deviations (y=a+bx) in models 1--6 or standard deviation for model 7 (a)
64 REAL PMF_GRID 8 2.0 0.5 20 36 18 0 180 1 # translation and rotation grid for PMF calculation
65 REAL RELATIVE_DIELECTRIC 1 1.0 # relative dielectric constant
66 REAL ROTATION_ANGLE 1 0.0 # rotation of MODEL around axis [degrees]
67 REAL ROTATION_AXIS 3 1.0 0.0 0.0 # rotation axis for MODEL
68 REAL SPLINE_DX 1 0.5 # interval size for splining restraints
69 REAL SPLINE_RANGE 1 4.0 # range of the splines
70 REAL GAP_PENALTIES_2D 8 0.35 1.2 0.9 1.2 0.6 8.6 1.2 0.0 # gap penalties for sequence/structure alignment: helix, beta, accessibility, straightness, and CA--CA distance factor, dst min, dst power, t ; best U,V=-450,0
71 REAL SCHEDULE_SCALE 33 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 # factors for physical restraint types in scaling the schedule
72 REAL CLUSTER_CUT 1 -1.0 # definition of a cluster
73 REAL GAP_PENALTIES_1D 2 -900 -50 # gap creation and extension penalties for sequence/sequence alignment
74 REAL FAST_SEARCH_CUTOFF 1 1.0 # if FAST_SEARCH is ON only sequences with database scan significance higher than this value are considered for randomization significance
75 REAL VIOL_REPORT_CUT2 33 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
76 REAL SIGNIF_CUTOFF 2 4.0 5.0 # cutoff for adding sequences to alignment, max difference from the best
77 REAL SEGMENT_CUTOFF 1 999999 # cutoff for writing out an alignment in SEGMENT_MATCHING
78 REAL FIX_OFFSETS 5 0. 1000. 2000. 3000. 4000. # offsets of the ALIGN2D alignment score for "fixed" positions indicated by ' 123456789' in line '_fix_pos'
79 REAL PSA_INTEGRATION_STEP 1 0.1 # integration step for WRITE_DATA
80 REAL ATOM_ACCESSIBILITY 1 1.0 # accessible atoms for MAKE_REGION
81 REAL PROBE_RADIUS 1 1.4 # probe_radius for WRITE_DATA
82 REAL REFERENCE_DISTANCE 1 3.5 # cutoff for selecting reference positions in SUPERPOSE
83 REAL SUBOPT_OFFSET 1 2.0 # offset for residue-residue score in getting suboptimals in ALIGN/ALIGN2D
1 INTEGER IO_UNIT 1 21 # IO unit for file operations
2 INTEGER ID1 1 1 # ID1 for filename construction
3 INTEGER ID2 1 1 # ID2 for filename construction
4 INTEGER NUMBER_PLACES 2 5 2 # pre- and post-decimal point places
5 INTEGER FILE_EXISTS 1 0 # an output flag: 0 | 1
6 INTEGER OUTPUT_CONTROL 5 1 0 1 1 0 # selects output, flow-control msgs, warnings, errors, dynamic mem msgs
7 INTEGER STOP_ON_ERROR 1 1 # whether to stop on error
8 INTEGER ERROR_STATUS 1 0 # application error status
9 INTEGER NUMBER_LINES 1 0 # number of lines in the newly opened file
31 INTEGER SCHEDULE_STEP 1 1 # schedule step for optimization
32 INTEGER ROUTINE_TYPE 1 1 # generic routine type for a miscellaneous command
33 INTEGER NLOGN_USE 1 15 # number of residues at which to begin using the N Log N non-bonded pairs routine
34 INTEGER SA_MOVSPERATM 1 30 #
35 INTEGER RESIDUE_GROUPING 1 1 #
36 INTEGER MAX_ITERATIONS 1 200 # maximal iterations in optimization
37 INTEGER RAND_SEED 1 -8123 # random seed from -50000 to -2
38 INTEGER COMPARE_MODE 1 3 # selects the type of comparison: 1 | 2 | 3
39 INTEGER EXTEND_HOT_SPOT 1 0 # whether to extend hot spots
40 INTEGER TOPOLOGY_MODEL 1 3 # selects topology library: 1--9
41 INTEGER RENUMBER_RESIDUES 0 # starting residue index for renumbering residues
42 INTEGER N_SCHEDULE 1 1 # the number of steps in the optimization schedule
43 INTEGER DISTANCE_RSR_MODEL 1 1 # the model for calculating distance restraints: 1--7
44 INTEGER ACCESSIBILITY_TYPE 1 8 # type of solvent accessibility: 1--10
45 INTEGER RESIDUE_SPAN_RANGE 2 0 99999 # range of residues spanning the allowed distances; for MAKE_RESTRAINTS, PICK_RESTRAINTS, non-bonded dynamic pairs
46 INTEGER MAX_GAP_LENGTH 1 999999 # maximal length of gap in protein comparisons
47 INTEGER OPTIMIZATION_METHOD 1 -999 # type of optimization method: 1 | 3
48 INTEGER GAP_EXTENSION 2 2 1 # extend insertions/deletions for that many residues, in PICK_ATOMS; don't select loops longer than i3
49 INTEGER NUMB_OF_SEQUENCES 1 1 # number of sequences in the alignment
50 INTEGER TRACE_OUTPUT 1 0 # modulus for writing information about optimization iterations: 0 for nothing
51 INTEGER SEARCH_TOP_LIST 1 20 # the length of the output hits list
52 INTEGER EQUILIBRATE 1 999999 # equilibrate during MD every that many steps
53 INTEGER MAX_GAPS_MATCH 1 1 #
54 INTEGER ALIGN_BLOCK 1 1 # the last sequence in the first block of sequences
55 INTEGER PICK_ATOMS_SET 1 1 # index of the selected atoms set: 1 | 2 | 3
56 INTEGER PMF_INDICES 0 0 0 0 0 #
57 INTEGER SEARCH_RANDOMIZATIONS 1 0 # number of randomizations for calculating the significance of a sequence/sequence similarity
58 INTEGER OFF_DIAGONAL 1 100 # to speed up the alignment
59 INTEGER RESTRAINT_GROUP 1 26 # physical restraint group
60 INTEGER OVERHANG 1 0 # un-penalized overhangs in protein comparisons
61 INTEGER SPLINE_SELECT 3 4 1 9 # specification of the restraints to be splined: {\tt form feature group}
62 INTEGER LIBRARY_SCHEDULE 1 1 # selects schedule from the $SCHED_LIB library
63 INTEGER NONBONDED_SEL_ATOMS 1 1 # a non-bonded pair has to have at least as many selected atoms
64 INTEGER SPLINE_MIN_POINTS 1 5 # have at least as many intervals in a spline
65 INTEGER SHEET_H-BONDS 1 7 # specify hydrogen bonds in a beta-sheet
66 INTEGER SMOOTHING_WINDOW 1 3 # profiles are smoothed over 2*SW + 1 residues
67 INTEGER RESTRAINT_SEL_ATOMS 1 1 # a restraint other than non-bonded pair has to have at least as many selected atoms
68 INTEGER N_SUBOPT 1 1 # number of optimal and suboptimal alignments ALIGN/ALIGN2D
69 INTEGER PROFILE_2D_PHYS 1 33 # 1 ... 33 physical type to be presented as 2D energy profile2
70 INTEGER MIN_LOOP_LENGTH 0 # inter-segment minimal lengths in SEGMENT_MATCHING
71 INTEGER SEGMENT_SHIFTS 0 # segment shifts +- in SEGMENT_MATCHING
72 INTEGER SEGMENT_REPORT 1 1D6 # for SEGMENT_MATCHING
73 INTEGER MNCH_LIB 1 1 # which MNCH lib to use in MAKE_RESTRAINTS
74 INTEGER SEGMENT_GROWTH_N 0 # reducing/growing segment N-termini in SEGMENT_MATCHING
75 INTEGER SEGMENT_GROWTH_C 0 # reducing/growing segment C-termini in SEGMENT_MATCHING
76 INTEGER EXPAND_CONTROL 5 9999 9999 1 10 0 # for controlling EXPAND_ALIGNMENT
77 INTEGER NUMB_OF_SEQUENCES2 1 0 # number of sequence in ALIGNMENT2
78 INTEGER MAXRES 0 0 # user specified maximal number of residues
79 INTEGER REGION_SIZE 1 20 # size of exposed region in MAKE_REGION
80 INTEGER MAX_LOOP_LENGTH 1 15 # maximal length of a loop in PICK_ATOMS
1 STRING OBJECTS 0 '' # variable names or constants
2 STRING VARIABLES 0 '' # variable names
3 STRING ROUTINE 0 '' # subroutine name
4 STRING ROOT_NAME 1 'undf' # root of a filename for filename construction
5 STRING DIRECTORY 1 '' # directory list (e.g., \Z{dir1:dir2:dir3:./:/})
6 STRING FILE_ID 1 'default' # file id for filename construction
7 STRING OPERATION 1 'SUM' # operation to perform: \Z{SUM} | \Z{MULTIPLY} | \Z{DIVIDE} | \Z{POWER} | \Z{MOD}
8 STRING RESULT 0 '' # variable name for the result of operation
9 STRING STRING_ARGUMENTS 0 '' # arguments for string operation
10 STRING OBJECTS_FILE 1 'top.out' # filename
11 STRING INCLUDE_FILE 1 '__mod' # include file name
12 STRING FILE 1 'default' # partial or complete filename
13 STRING RECORD 1 'undefined' # contents of the input line
14 STRING THEN 1 'undefined' # statement when IF evaluates to T
15 STRING ELSE 1 'undefined' # statement when IF evaluates to F
16 STRING COMMAND 1 'nothing' # UNIX command
17 STRING FILE_EXT 1 '' # file extension for filename construction
18 STRING OUTPUT_DIRECTORY 1 '' # output directory
19 STRING FILE_ACCESS 1 'SEQUENTIAL' # file access: \Z{SEQUENTIAL} | \Z{APPEND}
20 STRING FILE_STATUS 1 'UNKNOWN' # file status: \Z{UNKNOWN} | \Z{OLD} | \Z{NEW}
31 STRING BUILD_METHOD 1 'INTERNAL_COORDINATES' # method for building coordinates: \Z{INTERNAL_COORDINATES} | \Z{ONE_STICK} | \Z{TWO_STICKS} | \Z{3D_INTERPOLATION}
32 STRING DIHEDRALS 0 'PHI' 'PSI' 'CHI1' 'CHI2' 'CHI3' 'CHI4' # dihedral angle type selection: \Z{phi} | \Z{psi} | \Z{omega} | \Z{chi1} | \Z{chi2} | \Z{chi3} | \Z{chi4} | \Z{chi5} | \Z{alpha}
33 STRING RES_TYPES 1 'ALL' # residue type selection
34 STRING ATOM_TYPES 1 'ALL' # atom type selection
35 STRING VARIABILITY_FILE 1 'undefined' # output filename
36 STRING ALIGN_CODES 0 'all' # codes of proteins in the alignment
37 STRING ATOM_FILES 0 '' # complete or partial atom filenames
38 STRING OUTPUT 1 'LONG' # what and/or how to output
39 STRING CHANGE 1 'RANDOMIZE' # what to do: \Z{RANDOMIZE} | \Z{OPTIMIZE}
40 STRING FIT_ATOMS 1 'CA' # atom type(s) being superposed
41 STRING MODEL_FORMAT 0 'PDB' # selects input atom file format: \Z{PDB} | \Z{CHARMM} | \Z{UHBD}
42 STRING SEQUENCE 1 'undefined' # protein code in the alignment whose topology is constructed
43 STRING RESTRAINT_TYPE 0 'STEREO' # restraint type to be calculated: \Z{STEREO} | \Z{BOND} | \Z{ANGLE} | \Z{IMPROPER} | \Z{DIHEDRAL} | \Z{MRFP_STEREO} | \Z{MRFP_BOND} | \Z{MRFP_ANGLE} | \Z{MRFP_DIHEDRAL} | \Z{SPHERE} | \Z{SPHERE14} | \Z{LJ} | \Z{LJ14} | \Z{COULOMB} | \Z{COULOMB14} | \Z{ALPHA} | \Z{STRAND} | \Z{SHEET} | \Z{DISTANCE} | \Z{USER_DISTANCE} \Z{NONB_PAIR_SPLINE} | \Z{PHI-PSI_BINORMAL} | \Z{PHI-PSI_CLASS} | \Z{PHI_DIHEDRAL} | \Z{PSI_DIHEDRAL} | \Z{OMEGA_DIHEDRAL} | \Z{CHI1_DIHEDRAL} | \Z{CHI2_DIHEDRAL} | \Z{CHI3_DIHEDRAL} | \Z{CHI4_DIHEDRAL}
44 STRING ALIGNMENT_FORMAT 0 'PIR' # format of the alignment file: \Z{PIR} | \Z{PAP} | \Z{QUANTA} | \Z{INSIGHT} | \Z{FASTA}
45 STRING undefined81 0 ''
46 STRING ALIGNMENT_FEATURES 0 'INDICES CONSERVATION' # what alignment features to write out: \Z{ACCURACY} | \Z{HELIX} | \Z{BETA} | \Z{ACCESSIBILITY} | \Z{STRAIGHTNESS} | \Z{CONSERVATION} | \Z{INDICES} | \Z{ALL} | \Z{GAPS}
47 STRING RESIDUE_TYPE 1 'undefined' #
48 STRING MATRIX_FILE 1 'family.mat' # the filename of the pairwise distance matrix
49 STRING BASIS_PDF_WEIGHT 1 'LOCAL' # a method for calculation of basis pdf weights: \Z{LOCAL} | \Z{GLOBAL}
50 STRING DISTANCE_ATOMS 2 'CA' 'CA' # atom types for distance generation
51 STRING REFERENCE_ATOM 1 '' # reference atom name in SUPERPOSE
52 STRING undefined91 0 ''
53 STRING ATOM_IDS 0 '' # atom ids: \Z{atom:residue_id[:chain_id]}
54 STRING SPHERE_CENTER 2 'undefined' 'undefined' # '\#RES1:C' 'ATOM_NAME'
55 STRING SELECTION_MODE 1 'ATOM' # selecting what: \Z{ATOM} | \Z{RESIDUE}
56 STRING SELECTION_SEARCH 1 'SEGMENT' # search method: \Z{SPHERE} | \Z{SEGMENT}
57 STRING SELECTION_STATUS 1 'INITIALIZE' # what to do with selected atoms: \Z{ADD} | \Z{REMOVE} | \Z{INITIALIZE}
58 STRING SELECTION_SEGMENT 2 '' '' # \Z{RES:CHN} ids for the first and last residues in a chain/segment; or 'LOOPS'
59 STRING SELECTION_FROM 1 'ALL' # selecting from: \Z{ALL} | \Z{SELECTED}
60 STRING ALIGN_CODES2 0 'all' # align codes for alignment2
61 STRING MD_RETURN 1 'FINAL' # return MODEL with \Z{MINIMAL} energy or \Z{FINAL} MODEL
62 STRING ATOM_CLASSES_FILE 1 '$(LIB)/atmcls-melo.lib' # library with atom class definitions for MODELLER non-bonded restraints
63 STRING RR_FILE 1 '$(LIB)/as1.sim.mat' # input residue-residue scoring file
64 STRING SEARCH_CHAINS_FILE 1 '$(LIB)/CHAINS_all.seq' # file with a list of sequence codes
65 STRING MODEL_SEGMENT 2 'FIRST:@' 'LAST:' # segment to be read in
66 STRING MODEL2_SEGMENT 2 'FIRST:@' 'LAST:' # segment to be read in
67 STRING ATOM_FILES_DIRECTORY 1 './' # input atom files directory list (e.g., \Z{dir1:dir2:dir3:./:/})
68 STRING SEARCH_SORT 1 'LONGER' # which sequence to use for normalization when sorting the hit list: \Z{SHORTER} | \Z{LONGER}
69 STRING RESTRAINTS_FORMAT 1 'MODELLER' # format of the restraints file: \Z{MODELLER} | \Z{USER}
70 STRING SEARCH_CHAINS_LIST 1 '$(LIB)/CHAINS_3.0_40_XN.cod' # file with sequences
71 STRING SEGMENT_IDS 0 '' # new segment ids
72 STRING RESIDUE_IDS 0 '' # residue id (number:chnid)
73 STRING ALIGN_WHAT 1 'BLOCK' # what to align in ALIGN; \Z{BLOCK} | \Z{ALIGNMENT} | \Z{LAST}
74 STRING CLUSTER_METHOD 1 'RMSD' # what distance function to use in \C{CLUSTER}; \Z{RMSD} | \Z{MAXIMAL_DISTANCE}
75 STRING SEARCH_GROUP_LIST 1 '$(LIB)/CHAINS_3.0_40_XN.grp' # file with 40\% groups of sequences
76 STRING RESTYP_LIB_FILE 1 '$(LIB)/restyp.lib' # residue type library
77 STRING SWAP_ATOMS_IN_RES 1 '' # minimize RMS by swapping atoms in these residues (1 char code: 'DEFHLNQRVY')
78 STRING ATOM_FILES2 0 '' # complete or partial atom filenames for ALIGNMENT2
79 STRING INPUT_WEIGHTS_FILE 1 '' #
80 STRING OUTPUT_WEIGHTS_FILE 1 '' #
31 LOGICAL FIT 1 on # whether to do pairwise least-squares fitting or ALIGN2D alignment
32 LOGICAL SUPERPOSE_REFINE 1 off # whether to refine the superposition
35 LOGICAL DYNAMIC_SPHERE 1 on # whether to use dynamic soft-sphere repulsion terms
36 LOGICAL DYNAMIC_LENNARD 1 off # whether to use dynamic Lennard-Jones energy terms
37 LOGICAL DYNAMIC_COULOMB 1 off # whether to use dynamic Coulomb energy terms
38 LOGICAL WRITE_FIT 1 off # whether to write out fitted coordinates to .fit files
39 LOGICAL ASGL_OUTPUT 1 off # whether to write output for ASGL
40 LOGICAL ADD_RESTRAINTS 1 off # whether to add new restraints to existing restraints
41 LOGICAL ADD_SEGMENT 1 off # whether to add the new segments to the list of segments
42 LOGICAL REMOVE_GAPS 1 on # whether to remove all-gap positions in input alignment
44 LOGICAL LOCAL_ALIGNMENT 1 off # whether to do local as opposed to global alignment
45 LOGICAL WATER_IO 1 off # whether to read water coordinates
46 LOGICAL HETATM_IO 1 off # whether to read HETATM coordinates
47 LOGICAL HYDROGEN_IO 1 off # whether to read hydrogen coordinates
48 LOGICAL INITIALIZE_XYZ 1 on # whether to use IC entries to calculate all coordinates
49 LOGICAL ADD_SEQUENCE 1 off # whether to add the new sequences to the existing alignment
50 LOGICAL ALIGN3D_TRF 1 off # whether to transform the distances before dynamic programming
51 LOGICAL PATCH_DEFAULT 1 on # whether to do default NTER and CTER patching
52 LOGICAL INTERSEGMENT 1 on # whether to restrain inter-segment non-bonded pairs
53 LOGICAL ALIGN3D_REPEAT 1 off # do several starts to maximize number of equivalent positions
54 LOGICAL ALIGN_ALIGNMENT 1 off # writing out an alignment of alignments (for *)
55 LOGICAL INIT_VELOCITIES 1 on # whether to initialize velocities before MD
56 LOGICAL ADD_SYMMETRY 2 off on # whether to add segment pair, add atoms to segment pair
57 LOGICAL SPLINE_ON_SITE 1 off # whether to convert restraints to splines
58 LOGICAL ADD_PARAMETERS 1 off # whether to add new parameters to existing ones
59 LOGICAL ADD_TOPOLOGY 1 off # whether to add new residue topologies to existing ones
60 LOGICAL WRITE_WHOLE_PDB 1 on # whether to write out all lines in the input PDB file
61 LOGICAL WRITE_ALL_ATOMS 1 on # whether to write all atoms, even if unselected
62 LOGICAL CURRENT_DIRECTORY 1 on # whether to write output .fit files to current directory
63 LOGICAL DETAILED_DEBUGGING 1 off # whether to evaluate energy and derivatives wrt each restraint
64 LOGICAL DYNAMIC_PAIRS 1 off # whether to do dynamic pairs irrespective of anything
65 LOGICAL DYNAMIC_MODELLER 1 off # whether to use dynamic MODELLER non-bonded restraints
66 LOGICAL FAST_SEARCH 1 off # whether to use fast sequence search or not
67 LOGICAL DATA_FILE 1 off # whether results go to a separate file or not
68 LOGICAL NORMALIZE_PROFILE 1 off # whether to normalize energy/violations profiles or not, by the number of terms per residue
69 LOGICAL CUT_OVERHANGS 1 off # whether to cut overhangs at OVERHANG residues or not
70 LOGICAL RESIDUE_SPAN_SIGN 1 on # whether to do N*(N-1)/2 loop for atom pairs in MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance'
71 LOGICAL COVALENT_CYS 1 off # whether to consider SG-SG covalent bond similar to polypeptide chain when proximity of residues along the sequence is considered. If PATCH_SS_MODEL is done, then make it ON.
72 LOGICAL READ_WEIGHTS 1 off # whether to read the whole NxM weight matrix for ALIGN*
73 LOGICAL DYNAMIC_ACCESS 1 off # whether to use dynamic accessibility energy terms
74 LOGICAL DIH_LIB_ONLY 1 off # whether to use only library, not homologs for dihedral angle rsrs
75 LOGICAL NO_TER 1 off # whether to not write TER into PDB
76 LOGICAL WRITE_WEIGHTS 1 off # whether to write the whole NxM weight matrix for ALIGN*
77 LOGICAL EXCL_LOCAL 4 on on on on # whether to exclude bonds, angles, dihedrals, explicit excl pairs from the homology-derived distance rsrs
--- END OF FILE
The third column contains a number of values for each of the options if this
number is fixed, otherwise it contains 0.
You can change any command or variable name without changing the source code
relying on this file, but you can not change the order of the lines.