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Index

ACCESSIBILITY_TYPE: WRITE_DATA | MAKE_RESTRAINTS
ACCURACY_BORDER: WRITE_DATA
ADD_PARAMETERS: READ_PARAMETERS
ADD_RESTRAINT: Frequently asked questions (FAQ) | MAKE_RESTRAINTS | ADD_RESTRAINT | DELETE_RESTRAINT
ADD_RESTRAINTS: MAKE_RESTRAINTS | PICK_RESTRAINTS | READ_RESTRAINTS
ADD_SEGMENT: GENERATE_TOPOLOGY
ADD_SEQUENCE: READ_ALIGNMENT | SEQUENCE_TO_ALI
ADD_SYMMETRY: DEFINE_SYMMETRY
ADD_TOPOLOGY: READ_TOPOLOGY
ALIGN: Changes since release 6v2 | WRITE_ALIGNMENT | ALIGN | ALIGN2D | MALIGN | ALIGN_CONSENSUS | ALIGN3D
ALIGN2D: Changes since release 6v2 | Coordinate files and derivative | WRITE_ALIGNMENT | ALIGN | ALIGN2D
ALIGN3D: ALIGN | SUPERPOSE | ALIGN3D | MALIGN3D
ALIGN3D_REPEAT: ALIGN3D
ALIGN3D_TRF: ALIGN3D
ALIGN_ALIGNMENT: WRITE_ALIGNMENT
ALIGN_BLOCK: WRITE_ALIGNMENT | ALIGN | ALIGN2D | MALIGN | ALIGN_CONSENSUS | SEGMENT_MATCHING
ALIGN_CODES: GENERATE_TOPOLOGY | PATCH_SS_TEMPLATES | TRANSFER_RES_NUMB | WRITE_PDB_XREF | Alignment file format | READ_ALIGNMENT | CHECK_ALIGNMENT | SEQUENCE_TO_ALI | WRITE_ALIGNMENT | DESCRIBE | ID_TABLE | SEQUENCE_COMPARISON | SUPERPOSE | COMPARE | MALIGN3D | READ_PROFILE | SEQUENCE_SEARCH
ALIGN_CODES2: READ_ALIGNMENT2
ALIGN_CONSENSUS: WRITE_ALIGNMENT | ALIGN_CONSENSUS
ALIGN_WHAT: Changes since release 6v2 | ALIGN | ALIGN2D
alignment: Alignment file | Alignment file format
ALIGNMENT_FEATURES: WRITE_ALIGNMENT | SEQUENCE_SEARCH
ALIGNMENT_FORMAT: READ_ALIGNMENT | READ_ALIGNMENT2 | WRITE_ALIGNMENT | SEQUENCE_SEARCH | MAKE_CHAINS
ALN_TO_PROF: Changes since release 6v2 | ALN_TO_PROF | PROF_TO_ALN | READ_PROFILE | BUILD_PROFILE
APPEND_ALN: PROF_TO_ALN
ARGUMENTS: OPERATE | IF | Predefined TOP variables
ASGL_OUTPUT: COMPARE | ENERGY
atom classes: READ_ATOM_CLASSES | Script for modeling of
ATOM_ACCESSIBILITY: MAKE_REGION
ATOM_CLASSES_FILE: READ_ATOM_CLASSES
ATOM_FILES: GENERATE_TOPOLOGY | PATCH_SS_TEMPLATES | TRANSFER_XYZ | WRITE_PDB_XREF | Alignment file format | CHECK_ALIGNMENT | SEQUENCE_TO_ALI | WRITE_ALIGNMENT | DESCRIBE | COMPARE | MALIGN3D
ATOM_FILES_DIRECTORY: Input | Coordinate files and derivative | GENERATE_TOPOLOGY | PATCH_SS_TEMPLATES | READ_MODEL | READ_MODEL2 | TRANSFER_XYZ | WRITE_ALIGNMENT | EDIT_ALIGNMENT | DESCRIBE | COMPARE | MALIGN3D | MAKE_RESTRAINTS
ATOM_IDS: MAKE_RESTRAINTS | ADD_RESTRAINT | DELETE_RESTRAINT
ATOM_TYPES: PICK_ATOMS
BASE_ALIGN_CODES: EDIT_ALIGNMENT
BASIS_PDF_WEIGHT: MAKE_RESTRAINTS
BASIS_RELATIVE_WEIGHT: MAKE_RESTRAINTS
bibliography: MODELLER bibliography
BIN_LIB_FILE: MAKE_RESTRAINTS
BLOCK residues: Block (BLK) residues with
breakpoint: Controlling breakpoints and the
bug reports: Bug reports
BUILD_METHOD: BUILD_MODEL
BUILD_MODEL: Residues with defined topology, | GENERATE_TOPOLOGY | BUILD_MODEL | TRANSFER_XYZ | Flowchart of comparative modeling
BUILD_PROFILE: Changes since release 6v2 | READ_PROFILE | BUILD_PROFILE | READ_SEQUENCE_DB | WRITE_SEQUENCE_DB
CALL: CALL
CAP_ATOM_SHIFT: OPTIMIZE | Molecular dynamics
CHAINS_LIST: READ_SEQUENCE_DB | WRITE_SEQUENCE_DB
CHANGE: ROTATE_DIHEDRALS
CHECK_ALIGNMENT: Alignment file | Running MODELLER | Automated alignment and comparative | Frequently asked questions (FAQ) | CHECK_ALIGNMENT | Flowchart of comparative modeling
CHECK_PROFILE: BUILD_PROFILE
CHOP_NONSTD_TERMINII: MAKE_CHAINS
CLEAN_SEQUENCES: ALN_TO_PROF | READ_SEQUENCE_DB
CLOSE: CLOSE
CLOSE_FILE: Changes since release 6v2 | READ_ALIGNMENT
CLUSTER_CUT: TRANSFER_XYZ
CLUSTER_METHOD: TRANSFER_XYZ
COLOR_ALN_MODEL: COLOR_ALN_MODEL
COMMAND: SYSTEM | Predefined TOP variables
COMPARE: Coordinate files and derivative | DENDROGRAM | PRINCIPAL_COMPONENTS | COMPARE
COMPARE_ALIGNMENTS: READ_ALIGNMENT2 | COMPARE_ALIGNMENTS | SEQUENCE_TO_ALI | ALIGN
COMPARE_MODE: COMPARE
CONDENSE_RESTRAINTS: Frequently asked questions (FAQ) | MAKE_RESTRAINTS | PICK_RESTRAINTS | CONDENSE_RESTRAINTS | DELETE_RESTRAINT | REINDEX_RESTRAINTS
CONSENSUS_ALIGNMENT: WRITE_ALIGNMENT
CONTACT_SHELL: Formats of the restraints | MAKE_RESTRAINTS | ENERGY | OPTIMIZE | Atomic density
COULOMB_SWITCH: ENERGY | OPTIMIZE
COVALENT_CYS: ENERGY | OPTIMIZE
CURRENT_DIRECTORY: MALIGN3D
CUT_OVERHANGS: Changes since release 6v2
DATA_FILE: SEQUENCE_SEARCH
DEBUG_FUNCTION: DEBUG_FUNCTION
DEBUG_FUNCTION_CUTOFF: DEBUG_FUNCTION
DEFINE_INTEGER: DEFINE_INTEGER
DEFINE_LOGICAL: DEFINE_LOGICAL
DEFINE_REAL: DEFINE_REAL
DEFINE_STRING: DEFINE_STRING
DEFINE_SYMMETRY: DEFINE_SYMMETRY
DELETE_ALIGNMENT: DELETE_ALIGNMENT
DELETE_FILE: DELETE_FILE
DELETE_RESTRAINT: Frequently asked questions (FAQ) | DELETE_RESTRAINT
DENDROGRAM: TRANSFER_XYZ | ID_TABLE | DENDROGRAM | COMPARE | SEQUENCE_SEARCH
DESCRIBE: DESCRIBE
DETAILED_DEBUGGING: DEBUG_FUNCTION
DEVIATION: RANDOMIZE_XYZ | ROTATE_DIHEDRALS | Flowchart of comparative modeling
DIH_LIB_ONLY: MAKE_RESTRAINTS
DIHEDRALS: ROTATE_DIHEDRALS
DIRECTORY: Environment variables | Input | READ_TOPOLOGY | READ_PARAMETERS | READ_ALIGNMENT | READ_ALIGNMENT2 | SEQUENCE_COMPARISON | ALIGN | ALIGN2D | MALIGN | BUILD_PROFILE | SEQUENCE_SEARCH | SEQFILTER | READ_RESTRAINTS | READ_SCHEDULE | SWITCH_TRACE | SET | Predefined TOP variables
DISTANCE_ATOMS: PATCH_SS_TEMPLATES | COMPARE
DISTANCE_RSR_MODEL: MAKE_RESTRAINTS
DO: TOP Commands | DO
DO_LOOPS: Script for modeling of
DYNAMIC_ACCESS: ENERGY | OPTIMIZE
DYNAMIC_COULOMB: MAKE_RESTRAINTS | ENERGY | OPTIMIZE
DYNAMIC_LENNARD: MAKE_RESTRAINTS | ENERGY | OPTIMIZE
DYNAMIC_MODELLER: ENERGY | OPTIMIZE
DYNAMIC_SPHERE: MAKE_RESTRAINTS | ENERGY | OPTIMIZE
EDIT_ALIGN_CODES: EDIT_ALIGNMENT
EDIT_ALIGNMENT: Changes since release 6v2 | EDIT_ALIGNMENT
EDIT_FILE_EXT: Changes since release 6v2 | MALIGN3D
ELSE: IF | STRING_IF | Predefined TOP variables
END_DO: TOP Commands | DO
END_OF_FILE: Changes since release 6v2 | READ_ALIGNMENT
END_SUBROUTINE: TOP Commands | SUBROUTINE | END_SUBROUTINE
ENERGY: Frequently asked questions (FAQ) | GENERATE_TOPOLOGY | PICK_HOT_ATOMS | Formats of the restraints | DEFINE_SYMMETRY | SPLINE_RESTRAINTS | ENERGY | OPTIMIZE | DEBUG_FUNCTION | Flowchart of comparative modeling | Function
ENERGY_PROFILE: Changes between releases 4
EQUILIBRATE: OPTIMIZE | Molecular dynamics
EQUILIBRATION: OPTIMIZE
ERROR_STATUS: Predefined TOP variables
EXCL_LOCAL: MAKE_RESTRAINTS | ENERGY | OPTIMIZE
EXPAND_ALIGNMENT: EXPAND_ALIGNMENT | Flowchart of comparative modeling
EXPAND_CONTROL: EXPAND_ALIGNMENT
EXTEND_HOT_SPOT: PICK_HOT_ATOMS
FAST_SEARCH: SEQUENCE_SEARCH
FAST_SEARCH_CUTOFF: SEQUENCE_SEARCH
FILE: Automatic filename generation | READ_TOPOLOGY | READ_PARAMETERS | WRITE_TOPOLOGY_MODEL | READ_MODEL | READ_MODEL2 | WRITE_MODEL | WRITE_MODEL2 | WRITE_DATA | WRITE_PDB_XREF | READ_ALIGNMENT | READ_ALIGNMENT2 | WRITE_ALIGNMENT | PRINCIPAL_COMPONENTS | READ_PROFILE | WRITE_PROFILE | SEQUENCE_SEARCH | SEGMENT_MATCHING | READ_RESTRAINTS | WRITE_RESTRAINTS | READ_SCHEDULE | WRITE_SCHEDULE | ENERGY | SWITCH_TRACE | DELETE_FILE | WRITE_TOP | INQUIRE | Predefined TOP variables
file naming: File naming
file types: File types
FILE_ACCESS: OPEN | WRITE_TOP | Predefined TOP variables
FILE_EXISTS: INQUIRE | Predefined TOP variables
FILE_EXT: Environment variables | EXPAND_ALIGNMENT | SEGMENT_MATCHING | SET | Predefined TOP variables
FILE_ID: Environment variables | EXPAND_ALIGNMENT | SEGMENT_MATCHING | SET | Predefined TOP variables
FILE_STATUS: OPEN | Predefined TOP variables
FINAL_MALIGN3D: Flowchart of comparative modeling
FIT: WRITE_ALIGNMENT | ALIGN2D | SUPERPOSE | COMPARE | ALIGN3D | MALIGN3D
FIT_ATOMS: COMPARE | ALIGN3D | MALIGN3D
frequently asked questions: Frequently asked questions (FAQ)
GAP_EXTENSION: PICK_ATOMS
GAP_PENALTIES_1D: ALIGN | ALIGN2D | MALIGN | ALIGN_CONSENSUS | READ_PROFILE | WRITE_PROFILE | BUILD_PROFILE | SEQUENCE_SEARCH | SEQFILTER
GAP_PENALTIES_2D: ALIGN2D
GAP_PENALTIES_3D: ALIGN3D | MALIGN3D
GAP_POSITIONS: PICK_ATOMS
GAPS_IN_TARGET: BUILD_PROFILE
GENERATE_TOPOLOGY: Frequently asked questions (FAQ) | GENERATE_TOPOLOGY | PATCH | PATCH_SS_TEMPLATES | READ_MODEL | ROTATE_DIHEDRALS | MAKE_RESTRAINTS | Flowchart of comparative modeling
GO_TO: TOP Commands | GO_TO | LABEL | IF | STRING_IF
GRID_UNIT: WRITE_DATA
HETATM_IO: Block (BLK) residues with | GENERATE_TOPOLOGY | PATCH_SS_TEMPLATES | READ_MODEL | READ_MODEL2 | TRANSFER_XYZ | WRITE_ALIGNMENT | EDIT_ALIGNMENT
HYDROGEN_IO: GENERATE_TOPOLOGY | PATCH_SS_TEMPLATES | READ_MODEL | READ_MODEL2 | TRANSFER_XYZ | WRITE_ALIGNMENT | EDIT_ALIGNMENT
ID1: Environment variables | EXPAND_ALIGNMENT | SET | Predefined TOP variables
ID2: Environment variables | EXPAND_ALIGNMENT | SET | Predefined TOP variables
ID_TABLE: ID_TABLE | SEQUENCE_COMPARISON | DENDROGRAM | PRINCIPAL_COMPONENTS
IF: INQUIRE | IF
INCLUDE: Input | INCLUDE
INCLUDE_FILE: Input | INCLUDE | Predefined TOP variables
INIT_VELOCITIES: OPTIMIZE
INITIALIZE_XYZ: BUILD_MODEL
INPUT_PROFILE_FILE: Changes since release 6v2 | ALIGN2D
INPUT_WEIGHTS_FILE: ALIGN | ALIGN2D | ALIGN_CONSENSUS
INQUIRE: INQUIRE
installation: Installation
INTERSEGMENT: MAKE_RESTRAINTS
IO_UNIT: OPEN | WRITE | READ | CLOSE | Predefined TOP variables
IUPAC_MODEL: IUPAC_MODEL
LABEL: TOP Commands | GO_TO | LABEL
Lennard-Jones: Frequently asked questions (FAQ) | Residues with defined topology, | Block (BLK) residues with | READ_ATOM_CLASSES | GENERATE_TOPOLOGY | Formats of the restraints | MAKE_RESTRAINTS | PICK_RESTRAINTS | OPTIMIZE | Function | Lennard-Jones restraint
LENNARD_JONES_SWITCH: ENERGY | OPTIMIZE
LIBRARY_SCHEDULE: MAKE_SCHEDULE
LOCAL_ALIGNMENT: ALIGN | ALIGN2D | MALIGN | ALIGN3D | MALIGN3D | SEQUENCE_SEARCH
loop modeling: Script for modeling of
LOOP_ENDING_MODEL: Script for modeling of
LOOP_STARTING_MODEL: Script for modeling of
MAKE_CHAINS: Changes since release 6v2 | MAKE_CHAINS
MAKE_REGION: MAKE_REGION
MAKE_RESTRAINTS: Frequently asked questions (FAQ) | Changes since release 6v2 | Coordinate files and derivative | Residues with defined topology, | Block (BLK) residues with | PATCH_SS_TEMPLATES | PICK_ATOMS | Static and dynamic restraints | MAKE_RESTRAINTS | PICK_RESTRAINTS | SPLINE_RESTRAINTS | READ_RESTRAINTS | WRITE_RESTRAINTS | OPTIMIZE | Flowchart of comparative modeling
MAKE_SCHEDULE: MAKE_SCHEDULE | READ_SCHEDULE | WRITE_SCHEDULE | Flowchart of comparative modeling
MAKE_TOPOLOGY_MODEL: READ_TOPOLOGY | MAKE_TOPOLOGY_MODEL | WRITE_TOPOLOGY_MODEL
MALIGN: ALIGN | MALIGN | MALIGN3D | SEQUENCE_SEARCH
MALIGN3D: Changes since release 6v2 | Coordinate files and derivative | TRANSFER_XYZ | ALIGN | COMPARE | MALIGN3D | Flowchart of comparative modeling
MATRIX_FILE: ID_TABLE | SEQUENCE_COMPARISON | DENDROGRAM | PRINCIPAL_COMPONENTS | COMPARE
MATRIX_OFFSET: ALIGN | ALIGN2D | MALIGN | ALIGN3D | MALIGN3D | READ_PROFILE | WRITE_PROFILE | BUILD_PROFILE | SEQUENCE_SEARCH | SEQFILTER
MAX_ALN_EVALUE: BUILD_PROFILE
MAX_DIFF_RES: SEQFILTER
MAX_GAPS_MATCH: SEQUENCE_COMPARISON
MAX_ITERATIONS: OPTIMIZE
MAX_LOOP_LENGTH: Changes since release 6v2
MAX_NONSTDRES: MAKE_CHAINS
MAX_UNALIGNED_RES: SEQFILTER
MAXIMAL_DISTANCE: MAKE_RESTRAINTS
MD_RETURN: OPTIMIZE
MD_TIME_STEP: OPTIMIZE
MDT_LIB_FILE: MAKE_RESTRAINTS
method: Method for comparative protein
MIN_ATOM_SHIFT: OPTIMIZE
MIN_BASE_ENTRIES: EDIT_ALIGNMENT
MIN_LOOP_LENGTH: SEGMENT_MATCHING
MINIMAL_CHAIN_LENGTH: MAKE_CHAINS
MINIMAL_RESOLUTION: MAKE_CHAINS
MINIMAL_STDRES: MAKE_CHAINS
MINMAX_DB_SEQ_LEN: READ_SEQUENCE_DB
MINMAX_LOOP_LENGTH: Changes since release 6v2 | PICK_ATOMS
missing parameters: Frequently asked questions (FAQ) | Residues with defined topology,
MNCH_LIB: MAKE_RESTRAINTS
MODEL2_SEGMENT: READ_MODEL2
MODEL_FORMAT: READ_MODEL | READ_MODEL2 | WRITE_MODEL | WRITE_MODEL2
MODEL_SEGMENT: READ_MODEL | WRITE_PDB_XREF | Alignment file format
MODELLER_STATUS: Controlling breakpoints and the | READ_ALIGNMENT | READ_ALIGNMENT2 | ALIGN | ALIGN2D | MALIGN | ALIGN_CONSENSUS | ALIGN3D | MALIGN3D | BUILD_PROFILE | SEQUENCE_SEARCH | SEQFILTER | MAKE_CHAINS | OPTIMIZE
MOLPDF: ENERGY | OPTIMIZE
MUTATE_MODEL: MUTATE_MODEL | PICK_ATOMS
N_PROF_ITERATIONS: READ_PROFILE | BUILD_PROFILE
N_SCHEDULE: READ_SCHEDULE
NLOGN_USE: ENERGY | OPTIMIZE
NO_TER: WRITE_MODEL | WRITE_MODEL2
NONBONDED_SEL_ATOMS: MAKE_RESTRAINTS | PICK_RESTRAINTS | OPTIMIZE
NORMALIZE_PROFILE: ENERGY
NUMBER_LINES: OPEN
NUMBER_OF_STEPS: WRITE_DATA
NUMBER_PLACES: TOP Commands | WRITE | Predefined TOP variables
OBJECTS: WRITE | Predefined TOP variables
OBJECTS_FILE: OPEN | Predefined TOP variables
OFF_DIAGONAL: ALIGN | ALIGN2D | MALIGN | ALIGN3D | MALIGN3D | SEQUENCE_SEARCH
OPEN: OPEN
OPERATE: OPERATE
OPERATION: OPERATE | STRING_OPERATE | IF | STRING_IF | Predefined TOP variables
OPTIMIZATION_METHOD: OPTIMIZE
OPTIMIZE: GENERATE_TOPOLOGY | PICK_HOT_ATOMS | MAKE_RESTRAINTS | PICK_RESTRAINTS | ENERGY | OPTIMIZE | SWITCH_TRACE | Flowchart of comparative modeling | Function
ORIENT: WRITE_DATA
ORIENT_MODEL: ORIENT_MODEL | WRITE_DATA
OUTPUT: Changes between releases 4 | WRITE_DATA | COMPARE | ALIGN3D | MALIGN3D | SEQUENCE_SEARCH | DEFINE_SYMMETRY | ENERGY | OPTIMIZE
OUTPUT_COD_FILE: SEQFILTER
OUTPUT_CONTROL: Controlling breakpoints and the | READ_SEQUENCE_DB | Predefined TOP variables
OUTPUT_DIRECTORY: Output | WRITE_TOPOLOGY_MODEL | WRITE_MODEL | WRITE_MODEL2 | WRITE_PDB_XREF | SEQUENCE_TO_ALI | WRITE_ALIGNMENT | ID_TABLE | SEQUENCE_COMPARISON | SEGMENT_MATCHING | WRITE_RESTRAINTS | WRITE_SCHEDULE | WRITE | WRITE_TOP | Predefined TOP variables
OUTPUT_GRP_FILE: SEQFILTER
OUTPUT_PROFILE_FILE: Changes since release 6v2 | ALIGN2D
OUTPUT_SCORE_FILE: BUILD_PROFILE
OUTPUT_SCORES: BUILD_PROFILE
OUTPUT_WEIGHTS_FILE: ALIGN | ALIGN2D | ALIGN_CONSENSUS
OVERHANG: EDIT_ALIGNMENT | ALIGN | ALIGN2D | MALIGN | ALIGN3D | MALIGN3D | SEQUENCE_SEARCH
PATCH: Frequently asked questions (FAQ) | READ_TOPOLOGY | READ_PARAMETERS | GENERATE_TOPOLOGY | PATCH | DELETE_ALIGNMENT
PATCH_DEFAULT: GENERATE_TOPOLOGY | PATCH
PATCH_SS_MODEL: Frequently asked questions (FAQ) | PATCH_SS_MODEL
PATCH_SS_TEMPLATES: Frequently asked questions (FAQ) | PATCH_SS_TEMPLATES | PATCH_SS_MODEL | Flowchart of comparative modeling
PICK_ATOMS: Frequently asked questions (FAQ) | Changes since release 6v2 | Block (BLK) residues with | MUTATE_MODEL | PICK_ATOMS | SUPERPOSE | MAKE_RESTRAINTS | OPTIMIZE
PICK_ATOMS_SET: PICK_ATOMS
PICK_HOT_ATOMS: GENERATE_TOPOLOGY | PICK_HOT_ATOMS | Formats of the restraints | OPTIMIZE | Function
PICK_HOT_CUTOFF: PICK_HOT_ATOMS
PICK_RESTRAINTS: Frequently asked questions (FAQ) | PICK_ATOMS | PICK_HOT_ATOMS | DEFINE_SYMMETRY | PICK_RESTRAINTS | MAKE_SCHEDULE | READ_SCHEDULE | Flowchart of comparative modeling
PRINCIPAL_COMPONENTS: ID_TABLE | PRINCIPAL_COMPONENTS | COMPARE
PROBE_RADIUS: WRITE_DATA
PROF_TO_ALN: Changes since release 6v2 | PROF_TO_ALN | BUILD_PROFILE
PROFILE_FORMAT: READ_PROFILE | WRITE_PROFILE
program distribution: Distribution
program updates: MODELLER updates
PSA_INTEGRATION_STEP: WRITE_DATA
RADII_FACTOR: WRITE_DATA | MAKE_RESTRAINTS | ENERGY | OPTIMIZE
RAND_SEED: BUILD_MODEL | RANDOMIZE_XYZ | ROTATE_DIHEDRALS | MAKE_REGION | SEQUENCE_SEARCH | OPTIMIZE
RANDOMIZE: ROTATE_DIHEDRALS
RANDOMIZE_XYZ: PICK_ATOMS | RANDOMIZE_XYZ | MAKE_SCHEDULE | Flowchart of comparative modeling
RCUTL: WRITE_DATA
RCUTP: WRITE_DATA
READ: READ
READ_ALIGNMENT: Changes since release 6v2 | READ_ALIGNMENT | READ_ALIGNMENT2 | COMPARE_ALIGNMENTS | WRITE_ALIGNMENT | DESCRIBE | COMPARE | BUILD_PROFILE | Flowchart of comparative modeling
READ_ALIGNMENT2: READ_ALIGNMENT2 | COMPARE_ALIGNMENTS
READ_ATOM_CLASSES: READ_ATOM_CLASSES
READ_MODEL: Residues with defined topology, | GENERATE_TOPOLOGY | PATCH_SS_MODEL | READ_MODEL | READ_MODEL2 | WRITE_MODEL | WRITE_MODEL2 | BUILD_MODEL | ROTATE_DIHEDRALS | MAKE_CHAINS | CONDENSE_RESTRAINTS | Flowchart of comparative modeling
READ_MODEL2: READ_MODEL2
READ_PARAMETERS: READ_PARAMETERS
READ_PROFILE: Changes since release 6v2 | ALIGN2D | ALN_TO_PROF | PROF_TO_ALN | READ_PROFILE | BUILD_PROFILE | READ_SEQUENCE_DB
READ_RESTRAINTS: Frequently asked questions (FAQ) | READ_RESTRAINTS | WRITE_RESTRAINTS | Flowchart of comparative modeling
READ_RESTYP_LIB: Frequently asked questions (FAQ) | READ_RESTYP_LIB
READ_SCHEDULE: MAKE_SCHEDULE | READ_SCHEDULE | WRITE_SCHEDULE
READ_SEQUENCE_DB: Changes since release 6v2 | READ_PROFILE | READ_SEQUENCE_DB | SEQUENCE_SEARCH | SEQFILTER
READ_TOPOLOGY: READ_TOPOLOGY | ROTATE_DIHEDRALS
READ_WEIGHTS: ALIGN | ALIGN2D | ALIGN_CONSENSUS
RECORD: READ | Predefined TOP variables
REFERENCE_ATOM: SUPERPOSE
REFERENCE_DISTANCE: SUPERPOSE
REGION_SIZE: MAKE_REGION
REINDEX_RESTRAINTS: REINDEX_RESTRAINTS
RELATIVE_DIELECTRIC: ENERGY | OPTIMIZE | Coulomb restraint
REMOVE_GAPS: READ_ALIGNMENT | READ_ALIGNMENT2 | SEQUENCE_SEARCH
RENAME_SEGMENTS: RENAME_SEGMENTS
RENUMBER_RESIDUES: RENAME_SEGMENTS
REORDER_ATOMS: READ_MODEL2 | REORDER_ATOMS
RES_TYPES: PICK_ATOMS
RESET: RESET
RESIDUE_GROUPING: MAKE_RESTRAINTS
RESIDUE_IDS: Frequently asked questions (FAQ) | PATCH | MAKE_RESTRAINTS
RESIDUE_RANGE: PICK_RESTRAINTS
RESIDUE_SPAN_RANGE: MAKE_RESTRAINTS | PICK_RESTRAINTS | ENERGY | OPTIMIZE
RESIDUE_SPAN_SIGN: MAKE_RESTRAINTS | OPTIMIZE
RESIDUE_TYPE: PATCH | MUTATE_MODEL
RESTRAINT_PARAMETERS: MAKE_RESTRAINTS | ADD_RESTRAINT
RESTRAINT_SEL_ATOMS: MAKE_RESTRAINTS | PICK_RESTRAINTS
RESTRAINT_STDEV: MAKE_RESTRAINTS
RESTRAINT_STDEV2: Changes since release 6v2 | MAKE_RESTRAINTS
RESTRAINT_TYPE: Block (BLK) residues with | MAKE_RESTRAINTS | CONDENSE_RESTRAINTS
RESTRAINTS_FILTER: PICK_RESTRAINTS
RESTRAINTS_FORMAT: WRITE_RESTRAINTS
RESTYP_LIB_FILE: READ_RESTYP_LIB
RESULT: OPERATE | STRING_OPERATE | Predefined TOP variables
RETURN: RETURN | END_SUBROUTINE
REWIND_FILE: Changes since release 6v2 | READ_ALIGNMENT
RMS_CUTOFFS: SUPERPOSE | COMPARE
ROOT_NAME: Environment variables | EXPAND_ALIGNMENT | SEGMENT_MATCHING | SET | Predefined TOP variables
ROTATE_DIHEDRALS: PICK_ATOMS | ROTATE_DIHEDRALS
ROTATE_MODEL: ROTATE_MODEL
ROTATION_ANGLE: ROTATE_MODEL
ROTATION_AXIS: ROTATE_MODEL
ROTATION_MATRIX: ROTATE_MODEL
ROUTINE: CALL | SUBROUTINE | Predefined TOP variables
RR_FILE: SEQUENCE_COMPARISON | ALIGN | ALIGN2D | MALIGN | READ_PROFILE | WRITE_PROFILE | BUILD_PROFILE | SEQUENCE_SEARCH | SEQFILTER | SEGMENT_MATCHING
SCHEDULE_SCALE: MAKE_SCHEDULE | READ_SCHEDULE | ENERGY
SCHEDULE_STEP: ENERGY | OPTIMIZE
script file: Script file | Running MODELLER scripts
SEARCH_CHAINS_FILE: Changes since release 6v2
SEARCH_CHAINS_LIST: Changes since release 6v2
SEARCH_GROUP_LIST: SEQUENCE_SEARCH
SEARCH_RANDOMIZATIONS: SEQUENCE_SEARCH
SEARCH_SORT: SEQUENCE_SEARCH
SEARCH_TOP_LIST: SEQUENCE_SEARCH
SEGMENT_CUTOFF: SEGMENT_MATCHING
SEGMENT_GROWTH_C: SEGMENT_MATCHING
SEGMENT_GROWTH_N: SEGMENT_MATCHING
SEGMENT_IDS: RENAME_SEGMENTS
SEGMENT_MATCHING: Changes between releases 4 | SEGMENT_MATCHING
SEGMENT_REPORT: SEGMENT_MATCHING
SEGMENT_SHIFT: SEGMENT_MATCHING
SEGMENT_SHIFTS: SEGMENT_MATCHING
SELECTION_FROM: PICK_ATOMS
SELECTION_MODE: PICK_ATOMS | PICK_HOT_ATOMS
SELECTION_SEARCH: PICK_ATOMS
SELECTION_SEGMENT: PICK_ATOMS | Alignment file format
SELECTION_SLAB: PICK_ATOMS
SELECTION_STATUS: PICK_ATOMS
SEQ_DATABASE_FILE: READ_SEQUENCE_DB | WRITE_SEQUENCE_DB
SEQ_DATABASE_FORMAT: READ_SEQUENCE_DB | WRITE_SEQUENCE_DB | SEQFILTER
SEQFILTER: Changes since release 6v2 | READ_SEQUENCE_DB | SEQFILTER
SEQID_CUT: SEQFILTER
SEQUENCE: GENERATE_TOPOLOGY | ROTATE_DIHEDRALS
SEQUENCE_COMPARISON: ID_TABLE | SEQUENCE_COMPARISON | DENDROGRAM | PRINCIPAL_COMPONENTS
SEQUENCE_SEARCH: Changes since release 6v2 | SEQUENCE_SEARCH
SEQUENCE_TO_ALI: MUTATE_MODEL | SEQUENCE_TO_ALI
SET: Automatic filename generation | PATCH | SET
SET NLOGN_USE: OPTIMIZE
SHEET_H-BONDS: MAKE_RESTRAINTS
SIGNIF_CUTOFF: SEQUENCE_SEARCH
SMOOTH_PROF_WEIGHT: Changes since release 6v2 | ALIGN | ALIGN2D
SMOOTHING_WINDOW: ENERGY
SPHERE_CENTER: PICK_ATOMS
SPHERE_RADIUS: PICK_ATOMS
SPHERE_STDV: ENERGY | OPTIMIZE
SPLINE_DX: SPLINE_RESTRAINTS
SPLINE_MIN_POINTS: SPLINE_RESTRAINTS
SPLINE_ON_SITE: MAKE_RESTRAINTS
SPLINE_RANGE: SPLINE_RESTRAINTS
SPLINE_RESTRAINTS: SPLINE_RESTRAINTS
SPLINE_SELECT: SPLINE_RESTRAINTS
statistical potential: Script for modeling of
STOP: TOP Commands | STOP
STOP_ON_ERROR: Controlling breakpoints and the | READ_ALIGNMENT | READ_ALIGNMENT2 | ALIGN | ALIGN2D | MALIGN | ALIGN_CONSENSUS | ALIGN3D | MALIGN3D | BUILD_PROFILE | SEQUENCE_SEARCH | SEQFILTER | OPTIMIZE | Predefined TOP variables
STRING_ARGUMENTS: STRING_OPERATE | STRING_IF | Predefined TOP variables
STRING_IF: STRING_IF
STRING_OPERATE: STRING_OPERATE
STRUCTURE_TYPES: MAKE_CHAINS
SUBROUTINE: SUBROUTINE
SUPERPOSE: READ_MODEL2 | SUPERPOSE | COMPARE
SUPERPOSE_REFINE: SUPERPOSE
SURFTYP: WRITE_DATA
SWAP_ATOMS_IN_RES: SUPERPOSE
SWITCH_TRACE: OPTIMIZE | SWITCH_TRACE
SYMMETRY_WEIGHT: DEFINE_SYMMETRY
SYSTEM: SYSTEM
TEMPERATURE: OPTIMIZE
THEN: IF | STRING_IF | Predefined TOP variables
TIME_MARK: Changes since release 6v2 | TIME_MARK
TOPOLOGY_MODEL: Frequently asked questions (FAQ) | READ_TOPOLOGY | GENERATE_TOPOLOGY | PATCH | PATCH_SS_TEMPLATES | PATCH_SS_MODEL | MAKE_TOPOLOGY_MODEL | WRITE_DATA | MAKE_RESTRAINTS | ENERGY | OPTIMIZE
TRACE_OUTPUT: OPTIMIZE | SWITCH_TRACE
TRANSFER_RES_NUMB: READ_MODEL2 | TRANSFER_RES_NUMB
TRANSFER_XYZ: Residues with defined topology, | GENERATE_TOPOLOGY | BUILD_MODEL | TRANSFER_XYZ | MALIGN3D | Flowchart of comparative modeling
TRANSLATION: ROTATE_MODEL
tutorial: Tutorial on using MODELLER
UNBUILD_MODEL: UNBUILD_MODEL
UPDATE_DYNAMIC: ENERGY | OPTIMIZE
VARIABILITY_FILE: SEQUENCE_COMPARISON
VARIABLES: DEFINE_INTEGER | DEFINE_LOGICAL | DEFINE_REAL | DEFINE_STRING | Predefined TOP variables
VIOL_REPORT_CUT: PICK_HOT_ATOMS | ENERGY
VIOL_REPORT_CUT2: ENERGY
VOLUME: Changes since release 6v2
VOLUME_CAVITY: Changes since release 6v2
WATER_IO: GENERATE_TOPOLOGY | PATCH_SS_TEMPLATES | READ_MODEL | READ_MODEL2 | TRANSFER_XYZ | WRITE_ALIGNMENT | EDIT_ALIGNMENT
WEIGH_SEQUENCES: Changes since release 6v2 | ALIGN | ALIGN2D
WRITE: WRITE
WRITE_ALIGNMENT: Changes since release 6v2 | MUTATE_MODEL | WRITE_ALIGNMENT | ALIGN | ALIGN2D | ALIGN_CONSENSUS | MALIGN3D | BUILD_PROFILE | SEQUENCE_SEARCH
WRITE_ALL_ATOMS: WRITE_MODEL
WRITE_DATA: WRITE_DATA | MAKE_REGION
WRITE_FIT: MALIGN3D
WRITE_MODEL: WRITE_MODEL | WRITE_MODEL2 | Flowchart of comparative modeling
WRITE_MODEL2: WRITE_MODEL2
WRITE_PDB_XREF: WRITE_PDB_XREF
WRITE_PROFILE: Changes since release 6v2 | ALIGN2D | WRITE_PROFILE | BUILD_PROFILE
WRITE_RESTRAINTS: WRITE_RESTRAINTS | Flowchart of comparative modeling
WRITE_SCHEDULE: MAKE_SCHEDULE | WRITE_SCHEDULE
WRITE_SEQUENCE_DB: Changes since release 6v2 | WRITE_SEQUENCE_DB
WRITE_TOP: WRITE_TOP
WRITE_TOPOLOGY_MODEL: WRITE_TOPOLOGY_MODEL
WRITE_WEIGHTS: ALIGN | ALIGN2D | ALIGN_CONSENSUS
WRITE_WHOLE_PDB: MALIGN3D

Ben Webb 2004-10-04