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
29 TIME_MARK
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 undefined70
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 undefined70
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
107 MAKE_CHAINS
108 disabled7v7_1
109 BUILD_PROFILE
110 READ_SEQUENCE_DB
111 WRITE_SEQUENCE_DB
112 disabled7v7_2
113 READ_PROFILE
114 WRITE_PROFILE
115 ALN_TO_PROF
116 PROF_TO_ALN
117 VOLUME
118 VOLUME_CAVITY
119 EDIT_ALIGNMENT
120 SEQFILTER
121 DELETE_FILE
122 disabled7v7_3
--- 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 35 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 4.5 4.5 # 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 35 -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 -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 9 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, structure_profile ;
# best U,V=-450,0
71 REAL SCHEDULE_SCALE 35 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 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 35 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 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
84 REAL SMOOTH_PROF_WEIGHT 1 10 # for smoothing the profile aa frequency with a prior
85 REAL NEIGHBOR_CUTOFF 1 6.0 # for defining atom-atom contacts in WRITE_DATA
86 REAL MINIMAL_RESOLUTION 1 99.0 # resolution threshold to select chains
87 REAL GAP_PENALTIES 2 2. 0.5 # gap creation and extension penalties for SALIGN
88 REAL FEATURE_WEIGHTS 6 1. 0. 0. 0. 0. 0.# feature weights for SALIGN
89 REAL GAP-GAP_SCORE 1 0. # dissimilarity score for aligning gap with gap, in SALIGN
90 REAL GAP-RESIDUE_SCORE 1 0. # dissimilarity score for aligning gap with residue,
# in SALIGN
91 REAL GRID_UNIT 1 1. # grid size for cavities calculation in WRITE_DATA
92 REAL MIN_ALN_SEQ_ID 1 40. # minimal alignment sequence identity in BUILD_PROFILE
93 REAL RCUTP 1 3.0 # Radius of cut-off for a short sphere of atoms
94 REAL RCUTL 1 5.0 # Radius of cut-off for a long sphere of atoms
95 REAL RESTRAINT_STDEV2 3 0. 0. 0. # transforming standard deviation in models
# 3--6: S' = S + [ a + b max(0, c-g) ]
96 REAL MAX_ALN_EVALUE 1 0.1 # Max. E-value of alignments to include in BUILD_PROFILE
97 REAL VMIN 1 7.5 # Minimum volume [A^3] of a cluster of internal cavities
98 REAL RLINK 1 1.2 # Radius of cut-off to link in a cluster of internal cavities
99 REAL MATRIX_SCALING_FACTOR 1 0.0069 # substitution matrix scoring parameters, lambda
# and kappa - used by build_profile
100 REAL FILTER_VALUES 2 0. 0. # filter parameters for EM_GRID_SEARCH
101 REAL VOXEL_SIZE 1 0 # EM density map voxel size for EM_GRID_SEARCH
102 REAL RESOLUTION 1 0 # EM density map resolution for EM_GRID_SEARCH
103 REAL ANGULAR_STEP_SIZE 1 0 # Angular search step size in degrees for EM_GRID_SEARCH
104 REAL ALN_SCORE 1 -999 # Alignment score out put from the alignment routines
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--10
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 0 # 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 35 # 1 ... 35 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 MINMAX_LOOP_LENGTH 2 5 15 # minimal/maximal length of a loop in PICK_ATOMS
81 INTEGER MINIMAL_CHAIN_LENGTH 1 30 # length cut-off for selecting chains
82 INTEGER MINIMAL_STDRES 1 30 # min. number of standard residues
83 INTEGER NUMBER_OF_STEPS 1 1 # for calculating cavity volume
84 INTEGER MINMAX_DB_SEQ_LEN 2 0 999999 # minimal/maximal database sequence length
85 INTEGER N_PROF_ITERATIONS 1 3 # number of iterations in PROFILE_SEARCH
86 INTEGER MIN_ALN_LEN 1 50 # minimal number residues in alignment for BUILD_PROFILE
87 INTEGER MAXSEQ 1 0 # lower limit on the maximal number of sequences in alignment
88 INTEGER END_OF_FILE 1 0 # 0 | 1 whether or not reached end of file
# during READ_ALIGNMENT
89 INTEGER MIN_BASE_ENTRIES 1 1 # minimal number of templates in EDIT_ALIGNMENT
90 INTEGER SURFTYP 1 1 # Surface Type for accessibility calculations
# 1= contact; 2=surface
91 INTEGER SEQID_CUT 1 95 # Sequence Identity cut-off for SEQFILTER
92 INTEGER MAX_DIFF_RES 1 30 # Length cut-off for SEQFILTER
93 INTEGER MAX_UNALIGNED_RES 1 10 # Cut-off for number of unaligned residues in SEQFILTER
94 INTEGER MAX_NONSTDRES 1 10 # max. number of non-standard residues
95 INTEGER EM_MAP_SIZE 1 0 # size of the electron density map, for EM_GRID_SEARCH
96 INTEGER NUM_STRUCTURES 1 1 # number of structures to dock in EM_GRID_SEARCH
97 INTEGER BEST_DOCKED_MODELS 1 1 # number of best docked models to keep in EM_GRID_SEARCH
1 STRING OBJECTS 0 '' # variable names or constants
2 STRING VARIABLES 0 '' # variable names
3 STRING ROUTINE 1 '' # 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 or DOS 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 1 '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 1 '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 1 'PIR' # format of the alignment file: \Z{PIR} | \Z{PAP}
# | \Z{QUANTA} | \Z{INSIGHT} | \Z{FASTA}
45 STRING undefined81 1 ''
46 STRING ALIGNMENT_FEATURES 1 '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 1 ''
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}
# | \Z{SPHERE_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 '$(LIB)/as1.sim.mat' # input residue-residue scoring file
64 STRING SEQ_DATABASE_FILE 1 '$(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 CHAINS_LIST 1 '$(LIB)/CHAINS_3.0_40_XN.cod' # file with sequences
71 STRING SEGMENT_IDS 0 '' # new segment ids
72 STRING RESIDUE_IDS 0 '' # residue id (number:chnid)
73 STRING ALIGN_WHAT 1 'BLOCK' # what to align in ALIGN; \Z{BLOCK} | \Z{ALIGNMENT}
# | \Z{LAST} | \Z{PROFILE}
74 STRING CLUSTER_METHOD 1 'RMSD' # what distance function to use;
# \Z{RMSD} | \Z{MAXIMAL_DISTANCE}
75 STRING SEARCH_GROUP_LIST 1 '$(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 '' #
81 STRING INPUT_PROFILE_FILE 1 '' #
82 STRING OUTPUT_PROFILE_FILE 1 '' #
83 STRING STRUCTURE_TYPES 1 'structure' # 'structure structureX structureN structureM
# structureF structureE structureU'
84 STRING SEQ_DATABASE_FORMAT 1 'PIR' # 'PIR' 'FASTA' 'BINARY'; for READ/WRITE_SEQUENCE_DB
85 STRING PROFILE_FORMAT 1 'TEXT' # 'TEXT' | 'BINARY' ; for READ/WRITE_PROFILE
86 STRING PROFILE_LIST_FILE 1 '' # list of profiles for PROFILE_PROFILE_SCAN
87 STRING EDIT_ALIGN_CODES 0 'last' # codes of proteins in the alignment to be edited
88 STRING BASE_ALIGN_CODES 0 'rest' # codes of proteins in the alignment to be used as the base
89 STRING COMPARISON_TYPE 1 'MAT' # 'MAT' or 'PSSM' for comparing matrices or PSSMs when
# profiles are compared
90 STRING MATRIX_COMPARISON 1 'CC' # 'CC', 'MAX', 'AVE', - kinds of matrix comparisons
91 STRING TREE_TYPE 1 'DEFAULT' # 'DEFAULT', 'BUILD' - seq.tree types
# (default = malign)
92 STRING EDIT_FILE_EXT 2 '.pdb' '_fit.pdb' # old and new file extensions for filename
# construction in MALIGN3D
93 STRING ALIGNMENT_TYPE 1 'PROGRESSIVE' # 'PAIRWISE' 'TREE' 'PROGRESSIVE' for SALIGN
94 STRING RESIDUE_TYPE2 1 'REGULAR' # 'REGULAR' for 20 residues of 'GENERALIZED' otherwise
95 STRING WEIGHTS_TYPE 1 'SIMILAR' # or 'DISTANCE' -> for the kind of substitution values
96 STRING OUTPUT_GRP_FILE 1 'seqfilt.grp' # output file for seqfilter groups
97 STRING OUTPUT_COD_FILE 1 'seqfilt.cod' # output file for seqfilter representative groups
98 STRING OUTPUT_SCORE_FILE 1 'default' # output file for writing out individual scores in seqfilter
99 STRING EM_DENSITY_FORMAT 1 'XPLOR' # input electron density map file format for
# EM_GRID_SEARCH; \Z{MRC} | \Z{XPLOR}
100 STRING DOCK_ORDER 1 'INPUT' # order to dock proteins in EM_GRID_SEARCH;
# \Z{INPUT} | \Z{SIZE}
101 STRING START_TYPE 1 'CENTER' # how to start EM_GRID_SEARCH;
# \Z{CENTER} | \Z{ENTIRE} | \Z{SPECIFIC}
102 STRING TRANSLATE_TYPE 1 'NONE' # how to perform translations during EM_GRID_SEARCH;
# \Z{NONE} | \Z{RANDOM} | \Z{EXHAUSTIVE}
103 STRING FILTER_TYPE 1 'NONE' # how to filter the density during EM_GRID_SEARCH;
# \Z{NONE} | \Z{THRESHOLD} | \Z{THRESHOLD2} |
# \Z{SQUARE}
104 STRING EM_FIT_OUTPUT_FILE 1 '' # output file for EM_GRID_SEARCH
105 STRING EM_PDB_NAME 0 # PDB files to read for EM_GRID_SEARCH
106 STRING TARGET_PROFILE_FILE 1 '' # target_profile for profile_profile_scan
107 STRING DENSITY_TYPE 1 'SPHERE' # Function used to calculate density map cross-correlation
# in EM_GRID_SEARCH; \Z{SPHERE} | \Z{GAUSS} | \Z{HYBRID} |
# \Z{GAUSS_NORM} | \Z{TRACE}
108 STRING BKGRND_PRBLTY_FILE 1 '$(LIB)/blosum62_bkgrnd.prob' # background probability values for a
# residue-residue substitution matrix
109 STRING RR_IJ_FILE 1 '$(LIB)/blosum62.qij.mat' # input residue-residue target frquency file
110 STRING ALN_BASE_FILENAME 1 'alignment' # basename for construction of alignment filenames
# used by PROFILE_PROFILE_SCAN
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 not-used 1 off #
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
78 LOGICAL READ_PROFILE 1 off # whether to read str profile for ALIGN2D
79 LOGICAL WRITE_PROFILE 1 off # whether to write str profile for ALIGN2D
80 LOGICAL WEIGH_SEQUENCES 1 off # whether or not to weigh sequences in a profile
81 LOGICAL FOLLOW_TREE 1 off # whether or not to follow a tree for MALIGN3D
82 LOGICAL CHOP_NONSTD_TERMINII 1 on # whether or not to chop non-standard N- and/or
# C-terminal residue in MAKE_CHAINS
83 LOGICAL NORMALIZE_PP_SCORES 1 off # whether or not to normalize position-position
# scores in SALIGN
84 LOGICAL IMPROVE_ALIGNMENT 1 on # whether or not to optimize alignment in SALIGN
85 LOGICAL FIT_ON_FIRST 1 off # whether or not to optimize alignment in SALIGN
86 LOGICAL FIT_PDBNAM 1 on # whether or not to add _fit to the PDB file name
# in output alifile by SALIGN
87 LOGICAL ORIENT 1 off # whether or not to orient structure before volume
# calculation in WRITE_DATA
88 LOGICAL CLEAN_SEQUENCES 1 on # whether or not clean non-standard residues
89 LOGICAL CLOSE_FILE 1 on # whether or not to close the alignment file at the
# end of READ_ALIGNMENT
90 LOGICAL REWIND_FILE 1 off # whether or not to rewind the alignment file at the
# start of READ_ALIGNMENT
91 LOGICAL ACCURACY_BORDER 1 off # whether or not the closure on the surface accepts
# diagonal cords
92 LOGICAL GAP_FUNCTION 1 off # whether or not to switch on functional gap penalty
# in salign
93 LOGICAL SUBSTITUTION 1 off # whether to use the background in PSSM comparison
94 LOGICAL CHECK_PROFILE 1 on # whether to monitor profile degenration
95 LOGICAL OUTPUT_SCORES 1 off # whether to output individual scores in a build_profile scan
96 LOGICAL GAPS_IN_TARGET 1 off # whether to include gaps in target when using build_profile
97 LOGICAL APPEND_ALN 1 off # whether to append profiles to existing alignment arrays
98 LOGICAL SIMILARITY_FLAG 1 off # when turned on, the SALIGN command does not convert numbers
# into a distance sense.
99 LOGICAL SCORE_STATISTICS 1 on # PROFILE_PROFILE_SCAN: if turned off, the
# length-normalized z-scores are not computed
100 LOGICAL OUTPUT_ALIGNMENTS 1 on # PROFILE_PROFILE_SCAN: if turned off, no alignments will be
# written out.
--- 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.