--- KEYWORDS: 0 REAL ARGUMENTS 0 0.00 # real arguments to the math operation 32 REAL MATRIX_OFFSET 1 0.00 # substitution matrix offset for local alignment 33 REAL MATRIX_OFFSET_3D 1 -0.1 # substitution matrix offset for local alignment (RMS) 34 REAL VIOL_REPORT_CUT 39 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 4.5 999 999 999 999 # 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 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 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 39 -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 -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 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) 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 3.5 3.5 3.5 0.2 4.0 6.5 2.0 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=-100,0 71 REAL SCHEDULE_SCALE 39 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 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 39 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 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. -1. -2. -3. -4. # 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 0.0 # 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 105 REAL OVERHANG_FACTOR 1 0.4 # Factor to multiply seq. length diff with when auto_overhang is on 106 REAL DISTNGH 1 6.0 # Maximum distance to consider residues as neighbors 107 REAL CCMATRIX_OFFSET 1 -100 # Offset value for the scoring matrix in PPSCAN 107 REAL PX 1 0 # x origin of EM density map 108 REAL PY 1 0 # y origin of EM density map 109 REAL PZ 1 0 # z origin of EM density map 1 INTEGER IO_UNIT 1 30 # 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 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 41 INTEGER RENUMBER_RESIDUES 0 # starting residue index for renumbering residues 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 0 INTEGER NUMB_OF_SEQUENCES 1 0 # 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 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 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 0 # number of suboptimal alignments ALIGN/ALIGN2D 69 INTEGER PROFILE_2D_PHYS 1 35 # 1 ... 39 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 1000000 # 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 0 INTEGER NUMB_OF_SEQUENCES2 1 0 # number of sequence in ALIGNMENT2 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 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 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 98 INTEGER OVERHANG_AUTO_LIMIT 1 60 # auto_overhang effective if seq length diff greater than overhang_auto_limit 99 INTEGER CHAINS_NUM 0 1 # number of chains in input pdb filein EM_GRID_SEARCH 100 INTEGER NSEGM 1 2 # number of segments for DRMS computation 1 STRING OBJECTS 0 '' # variable names or constants 0 STRING VARIABLES 0 '' # variable names 0 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 0 STRING OPERATION 1 'SUM' # operation to perform: \Z{SUM} | \Z{MULTIPLY} # | \Z{DIVIDE} | \Z{POWER} | \Z{MOD} 0 STRING RESULT 0 '' # variable name for the result of operation 0 STRING STRING_ARGUMENTS 0 '' # arguments for string operation 10 STRING OBJECTS_FILE 1 'top.out' # filename 0 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 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{SPHERE} # | \Z{SPHERE14} | \Z{LJ} | \Z{LJ14} | \Z{COULOMB} # | \Z{COULOMB14} | \Z{DISTANCE} | \Z{USER_DISTANCE} # | \Z{NONB_PAIR_SPLINE} | \Z{PHI-PSI_BINORMAL} # | \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} 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 68 STRING SEARCH_SORT 1 'LONGER' # which sequence to use for normalization when # sorting the hit list: \Z{SHORTER} | \Z{LONGER} 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 '' # Exteral weight matrix input to MODELLER (SALIGN/ALIGN) 80 STRING OUTPUT_WEIGHTS_FILE 1 '' # File into which the weight file is wriiten (iff WRITE_WEIGHTS = 'on') 81 STRING INPUT_PROFILE_FILE 1 '' # multiple sequece alignment read into MODELLER for profile-profile alignments 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 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} | Z{LAPLACIAN} # \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 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 111 STRING ASSESS_METHOD 1 '' # ASSESS_MODEL: assessment method to use 112 STRING PSSM_WEIGHTS_TYPE 1 'HH1' # type of weighting to calculate pssm; \Z{HH0} | \Z{HH1} | # \Z{PSIC} 113 STRING SUMMARY_FILE 1 'ppscan.sum' # output file for writing PPSCAN summary 114 STRING DENDROGRAM_FILE 1 '' # File into which the SALIGN dendrogram is written out 115 STRING PSSM_FILE 1 'buildp.pssm' # File into which the BUILD_PROFILE PSSM is written out 116 STRING PSSMDB_NAME 1 'profiles.pssm' # Filename for PSSM database 117 STRING DNR_ACCPT_LIB 1 '' 118 STRING EXT_TREE_FILE 1 '' # To read a pre computed tree for SALIGN 119 STRING CC_FUNC_TYPE 1 'CCF' # Type of cross-correlation to use for EM density 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 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 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 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 70 LOGICAL RESIDUE_SPAN_SIGN 1 on # whether to do N*(N-1)/2 loop for atom pairs in # MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance' 72 LOGICAL READ_WEIGHTS 1 off # whether to read the whole NxM weight matrix for ALIGN* 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* 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 all structures are to be fit on the first structure, given the final alignment 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. 101 LOGICAL REFINE_LOCAL 1 on # whether to refine superposition using locally similar # substructures 102 LOGICAL WRITE_SUMMARY 1 on # whether to write summary information for PPSCAN 103 LOGICAL AUTO_OVERHANG 1 off # overhang values made dependent on sequence length difference 104 LOGICAL WRITE_PSSM 1 off # flag to write out the PSSM into the log file --- 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.