Index

ACCESSIBILITY_TYPE

WRITE_DATA write | WRITE_DATA write | WRITE_DATA write | MAKE_RESTRAINTS make

ADD_PARAMETERS

READ_PARAMETERS read | READ_PARAMETERS read

ADD_RESTRAINT

Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Detailed chronological listing of | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | ADD_RESTRAINT add | DELETE_RESTRAINT unselect

ADD_RESTRAINTS

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | READ_RESTRAINTS read | READ_RESTRAINTS read

ADD_SEGMENT

GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate

ADD_SEQUENCE

READ_ALIGNMENT read | READ_ALIGNMENT read | SEQUENCE_TO_ALI copy | SEQUENCE_TO_ALI copy

ADD_SYMMETRY

DEFINE_SYMMETRY define | DEFINE_SYMMETRY define | DEFINE_SYMMETRY define | DEFINE_SYMMETRY define

ADD_TOPOLOGY

READ_TOPOLOGY read | READ_TOPOLOGY read

ALIGN

Preparing an initial family | WRITE_ALIGNMENT write | ALIGN align | ALIGN2D align | MALIGN align | MALIGN align | ALIGN_CONSENSUS consensus | ALIGN3D align

ALIGN2D

Preparing an initial family | Detailed chronological listing of | Coordinate files and derivative | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | ALIGN align | ALIGN2D align | ALIGN2D align

ALIGN3D

ALIGN align | SUPERPOSE superpose | ALIGN3D align | MALIGN3D align

ALIGN3D_REPEAT

ALIGN3D align | ALIGN3D align

ALIGN3D_TRF

ALIGN3D align | ALIGN3D align

ALIGN_ALIGNMENT

Detailed chronological listing of | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write

ALIGN_BLOCK

Detailed chronological listing of | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | ALIGN align | ALIGN align | ALIGN align | ALIGN align | ALIGN2D align | MALIGN align | MALIGN align | ALIGN_CONSENSUS consensus | SEGMENT_MATCHING align | SEGMENT_MATCHING align | SEGMENT_MATCHING align

ALIGN_CODES

Detailed chronological listing of | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_TEMPLATES guess | TRANSFER_RES_NUMB residue | TRANSFER_RES_NUMB residue | WRITE_PDB_XREF write | Alignment file format | READ_ALIGNMENT read | READ_ALIGNMENT read | CHECK_ALIGNMENT check | SEQUENCE_TO_ALI copy | SEQUENCE_TO_ALI copy | WRITE_ALIGNMENT write | DESCRIBE describe | DESCRIBE describe | ID_TABLE calculate | ID_TABLE calculate | SEQUENCE_COMPARISON compare | SUPERPOSE superpose | SUPERPOSE superpose | COMPARE compare | COMPARE compare | COMPARE compare | COMPARE compare | MALIGN3D align | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

ALIGN_CODES2

Detailed chronological listing of | READ_ALIGNMENT2 read

ALIGN_CONSENSUS

WRITE_ALIGNMENT write | ALIGN_CONSENSUS consensus

ALIGN_WHAT

ALIGN align | ALIGN align | ALIGN align

alignment

Preparing an initial family | Becoming familiar with the | Alignment file | Alignment file format

ALIGNMENT_FEATURES

WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | SEQUENCE_SEARCH search

ALIGNMENT_FORMAT

Detailed chronological listing of | READ_ALIGNMENT read | READ_ALIGNMENT2 read | WRITE_ALIGNMENT write | SEQUENCE_SEARCH search

ARGUMENTS

OPERATE perform | Predefined TOP variables

ASGL_2D_OUTPUT

Detailed chronological listing of

ASGL_2D_TYPE

Detailed chronological listing of

ASGL_OUTPUT

COMPARE compare | COMPARE compare | ENERGY evaluate | ENERGY evaluate

ATOM_ACCESSIBILITY

MAKE_REGION define | MAKE_REGION define

ATOM_CLASSES_FILE

READ_ATOM_CLASS read | READ_ATOM_CLASS read

ATOM_FILES

GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_TEMPLATES guess | PATCH_SS_TEMPLATES guess | TRANSFER_XYZ copy | WRITE_PDB_XREF write | Alignment file format | CHECK_ALIGNMENT check | SEQUENCE_TO_ALI copy | SEQUENCE_TO_ALI copy | WRITE_ALIGNMENT write | DESCRIBE describe | DESCRIBE describe | COMPARE compare | COMPARE compare | COMPARE compare | COMPARE compare | MALIGN3D align | MALIGN3D align

ATOM_FILES_DIRECTORY

Input. | Coordinate files and derivative | Coordinate files and derivative | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_TEMPLATES guess | READ_MODEL read | READ_MODEL2 read | TRANSFER_XYZ copy | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | DESCRIBE describe | COMPARE compare | MALIGN3D align | MAKE_RESTRAINTS make

ATOM_IDS

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | ADD_RESTRAINT add | DELETE_RESTRAINT unselect | DELETE_RESTRAINT unselect

ATOM_TYPES

PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select

BASIS_PDF_WEIGHT

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

BASIS_RELATIVE_WEIGHT

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

bibliography

MODELLER bibliography

BIN_LIB_FILE

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

BLOCK residues

Block (BLK) residues with

breakpoint

Controlling breakpoints and the

bug reports

Bug reports

BUILD

Detailed chronological listing of

BUILD_METHOD

Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | BUILD_MODEL build | BUILD_MODEL build | BUILD_MODEL build | BUILD_MODEL build | BUILD_MODEL build | BUILD_MODEL build

BUILD_MODEL

Detailed chronological listing of | Residues with defined topology, | GENERATE_TOPOLOGY generate | BUILD_MODEL build | TRANSFER_XYZ copy | Flowchart of comparative modeling

CALL

CALL call

CAP_ATOM_SHIFT

OPTIMIZE optimize | OPTIMIZE optimize | Molecular dynamics

CHANGE

ROTATE_DIHEDRALS change | ROTATE_DIHEDRALS change | ROTATE_DIHEDRALS change | ROTATE_DIHEDRALS change

CHECK_ALIGNMENT

Becoming familiar with the | Alignment file | Running MODELLER | Fully automated comparative modeling | Frequently asked questions (FAQ) | CHECK_ALIGNMENT check | Flowchart of comparative modeling

CLOSE

CLOSE close

CLUSTER

TRANSFER_XYZ copy

CLUSTER_CUT

TRANSFER_XYZ copy | TRANSFER_XYZ copy | TRANSFER_XYZ copy | TRANSFER_XYZ copy

CLUSTER_METHOD

Detailed chronological listing of | TRANSFER_XYZ copy | TRANSFER_XYZ copy | TRANSFER_XYZ copy

COLOR_ALN_MODEL

COLOR_ALN_MODEL color

COMMAND

SYSTEM execute | Predefined TOP variables

COMPARE

Detailed chronological listing of | Coordinate files and derivative | DENDROGRAM clustering | PRINCIPAL_COMPONENTS clustering | COMPARE compare | COMPARE compare

COMPARE_ALIGNMENTS

READ_ALIGNMENT2 read | COMPARE_ALIGNMENTS compare | SEQUENCE_TO_ALI copy | ALIGN align

COMPARE_MODE

COMPARE compare | COMPARE compare

COMPARE_SEQUENCES

Selecting the templates | Detailed chronological listing of

CONDENSE_RESTRAINTS

Frequently asked questions (FAQ) | MAKE_RESTRAINTS make | PICK_RESTRAINTS pick | CONDENSE_RESTRAINTS remove | DELETE_RESTRAINT unselect | REINDEX_RESTRAINTS renumber

CONSENSUS_ALIGNMENT

WRITE_ALIGNMENT write

CONTACT_SHELL

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

COULOMB_SWITCH

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

COVALENT_CYS

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

CURRENT_DIRECTORY

MALIGN3D align | MALIGN3D align

CUT_OVERHANGS

WRITE_ALIGNMENT write | WRITE_ALIGNMENT write

DATA_FILE

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

DEBUG_FUNCTION

DEBUG_FUNCTION test

DEBUG_FUNCTION_CUTOFF

DEBUG_FUNCTION test | DEBUG_FUNCTION test | DEBUG_FUNCTION test | DEBUG_FUNCTION test

DEFINE_INTEGER

DEFINE_INTEGER define

DEFINE_LOGICAL

DEFINE_LOGICAL define

DEFINE_REAL

DEFINE_REAL define

DEFINE_STRING

DEFINE_STRING define

DEFINE_SYMMETRY

DEFINE_SYMMETRY define | DEFINE_SYMMETRY define | DEFINE_SYMMETRY define

DELETE_ALIGNMENT

DELETE_ALIGNMENT delete

DELETE_RESTRAINT

Frequently asked questions (FAQ) | DELETE_RESTRAINT unselect | DELETE_RESTRAINT unselect

DENDROGRAM

Selecting the templates | TRANSFER_XYZ copy | ID_TABLE calculate | DENDROGRAM clustering | COMPARE compare | SEQUENCE_SEARCH search

DESCRIBE

DESCRIBE describe | DESCRIBE describe

DETAILED_DEBUGGING

DEBUG_FUNCTION test | DEBUG_FUNCTION test

DEVIATION

RANDOMIZE_XYZ randomize | RANDOMIZE_XYZ randomize | RANDOMIZE_XYZ randomize | ROTATE_DIHEDRALS change | Flowchart of comparative modeling

DIH_LIB_ONLY

Detailed chronological listing of | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

DIHEDRALS

ROTATE_DIHEDRALS change | ROTATE_DIHEDRALS change

DIRECTORY

Environment variables | Input. | Input. | Input. | Input. | Input. | READ_TOPOLOGY read | READ_TOPOLOGY read | READ_PARAMETERS read | READ_PARAMETERS read | READ_ALIGNMENT read | READ_ALIGNMENT2 read | SEQUENCE_COMPARISON compare | ALIGN align | ALIGN2D align | MALIGN align | SEQUENCE_SEARCH search | READ_RESTRAINTS read | READ_SCHEDULE read | SWITCH_TRACE open | SET set | Predefined TOP variables

DISTANCE_ATOMS

PATCH_SS_TEMPLATES guess | PATCH_SS_TEMPLATES guess | COMPARE compare | COMPARE compare

DISTANCE_RSR_MODEL

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

DO

TOP Commands | DO DO | DO DO

DO_LOOPS

Script for modeling of

DYNAMIC_ACCESS

Detailed chronological listing of | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

DYNAMIC_COULOMB

MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

DYNAMIC_FLAG

Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of

DYNAMIC_LENNARD

MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

DYNAMIC_MODELLER

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

DYNAMIC_SPHERE

MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

ELSE

IF conditional | STRING_IF conditional | STRING_IF conditional | Predefined TOP variables

END_DO

TOP Commands | DO DO

END_SUBROUTINE

TOP Commands | SUBROUTINE define | END_SUBROUTINE end

ENERGY

Evaluating the models | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Detailed chronological listing of | Detailed chronological listing of | GENERATE_TOPOLOGY generate | PICK_HOT_ATOMS pick | PICK_HOT_ATOMS pick | Formats of the restraints | DEFINE_SYMMETRY define | SPLINE_RESTRAINTS approximate | ENERGY evaluate | ENERGY evaluate | ENERGY evaluate | OPTIMIZE optimize | DEBUG_FUNCTION test | DEBUG_FUNCTION test | Flowchart of comparative modeling | Function

ENERGY_PROFILE

Major changes in Releases | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of

EQUILIBRATE

OPTIMIZE optimize | Molecular dynamics

EQUILIBRATION

OPTIMIZE optimize

ERROR_STATUS

Detailed chronological listing of | Predefined TOP variables

evaluation, model

Evaluating the models

EXCL_LOCAL

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

EXPAND_ALIGNMENT

Detailed chronological listing of | EXPAND_ALIGNMENT put | Flowchart of comparative modeling

EXPAND_CONTROL

Detailed chronological listing of | EXPAND_ALIGNMENT put

EXTEND_HOT_SPOT

PICK_HOT_ATOMS pick | PICK_HOT_ATOMS pick

FAST_SEARCH

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

FAST_SEARCH_CUTOFF

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

FILE

Detailed chronological listing of | Automatic filename generation | READ_TOPOLOGY read | READ_TOPOLOGY read | READ_PARAMETERS read | READ_PARAMETERS read | WRITE_TOPOLOGY_MODEL write | READ_MODEL read | READ_MODEL2 read | WRITE_MODEL write | WRITE_MODEL2 write | WRITE_DATA write | WRITE_DATA write | WRITE_PDB_XREF write | READ_ALIGNMENT read | READ_ALIGNMENT2 read | WRITE_ALIGNMENT write | PRINCIPAL_COMPONENTS clustering | PRINCIPAL_COMPONENTS clustering | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEGMENT_MATCHING align | SEGMENT_MATCHING align | READ_RESTRAINTS read | WRITE_RESTRAINTS write | READ_SCHEDULE read | WRITE_SCHEDULE write | SWITCH_TRACE open | WRITE_TOP write | INQUIRE check | Predefined TOP variables

file naming

File naming

file types

File types

FILE_ACCESS

OPEN open | OPEN open | WRITE_TOP write | Predefined TOP variables

FILE_EXISTS

INQUIRE check | Predefined TOP variables

FILE_EXT

Environment variables | Environment variables | EXPAND_ALIGNMENT put | EXPAND_ALIGNMENT put | SEGMENT_MATCHING align | SEGMENT_MATCHING align | SET set | SET set | Predefined TOP variables

FILE_FORMAT

READ_RESTRAINTS read | WRITE_RESTRAINTS write

FILE_ID

Environment variables | Environment variables | Environment variables | Environment variables | Environment variables | EXPAND_ALIGNMENT put | EXPAND_ALIGNMENT put | SEGMENT_MATCHING align | SEGMENT_MATCHING align | SET set | SET set | SET set | SET set | SET set | Predefined TOP variables

FILE_STATUS

OPEN open | OPEN open | Predefined TOP variables

FINAL_MALIGN3D

Detailed chronological listing of | Flowchart of comparative modeling

FIT

WRITE_ALIGNMENT write | ALIGN2D align | ALIGN2D align | SUPERPOSE superpose | SUPERPOSE superpose | COMPARE compare | COMPARE compare | ALIGN3D align | ALIGN3D align | MALIGN3D align | MALIGN3D align | MALIGN3D align

FIT_ATOMS

COMPARE compare | COMPARE compare | ALIGN3D align | ALIGN3D align | MALIGN3D align | MALIGN3D align | MALIGN3D align

GAP_EXTENSION

Detailed chronological listing of | PICK_ATOMS select | PICK_ATOMS select

GAP_PENALTIES_1D

ALIGN align | ALIGN align | ALIGN align | ALIGN2D align | ALIGN2D align | MALIGN align | MALIGN align | ALIGN_CONSENSUS consensus | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

GAP_PENALTIES_2D

ALIGN2D align | ALIGN2D align | ALIGN2D align

GAP_PENALTIES_3D

ALIGN3D align | ALIGN3D align | ALIGN3D align | ALIGN3D align | MALIGN3D align | MALIGN3D align | MALIGN3D align | MALIGN3D align

GAP_POSITIONS

PICK_ATOMS select | PICK_ATOMS select

GENERATE_TOPOLOGY

Frequently asked questions (FAQ) | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH patch | PATCH patch | PATCH_SS_TEMPLATES guess | READ_MODEL read | ROTATE_DIHEDRALS change | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | Flowchart of comparative modeling

GO_TO

TOP Commands | GO_TO jump | LABEL place | IF conditional | STRING_IF conditional

HETATM_IO

GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_TEMPLATES guess | READ_MODEL read | READ_MODEL2 read | TRANSFER_XYZ copy | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write

HYDROGEN_IO

GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_TEMPLATES guess | READ_MODEL read | READ_MODEL2 read | TRANSFER_XYZ copy | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write

ID1

Environment variables | Environment variables | Environment variables | EXPAND_ALIGNMENT put | SET set | SET set | SET set | Predefined TOP variables

ID2

Environment variables | Environment variables | Environment variables | EXPAND_ALIGNMENT put | SET set | SET set | SET set | Predefined TOP variables

ID_TABLE

Selecting the templates | Detailed chronological listing of | ID_TABLE calculate | SEQUENCE_COMPARISON compare | DENDROGRAM clustering | DENDROGRAM clustering | PRINCIPAL_COMPONENTS clustering | PRINCIPAL_COMPONENTS clustering

IDEAL_ENERGY1

Detailed chronological listing of

IF

INQUIRE check | IF conditional

INCLUDE

Input. | INCLUDE include | INCLUDE include

INCLUDE_FILE

Input. | INCLUDE include | INCLUDE include | Predefined TOP variables

INHERIT_DISULFIDES

Detailed chronological listing of

INIT_VELOCITIES

OPTIMIZE optimize | OPTIMIZE optimize

INITIALIZE_XYZ

BUILD_MODEL build | BUILD_MODEL build

INPUT_WEIGHTS_FILE

ALIGN align | ALIGN2D align | ALIGN_CONSENSUS consensus

INQUIRE

INQUIRE check

installation

Installation

INTERSEGMENT

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

IO_UNIT

OPEN open | WRITE write | READ read | READ read | CLOSE close | Predefined TOP variables

IUPAC_MODEL

IUPAC_MODEL standardize

KEEP_RESTRAINTS

Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of

LABEL

TOP Commands | GO_TO jump | LABEL place

LENNARD_JONES_SWITCH

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

LENNARD_JONES_SWITCH[2]

OPTIMIZE optimize

LIBRARY_SCHEDULE

MAKE_SCHEDULE create | MAKE_SCHEDULE create

LOCAL_ALIGNMENT

ALIGN align | ALIGN align | ALIGN align | ALIGN2D align | MALIGN align | ALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search

MAKE_REGION

MAKE_REGION define | MAKE_REGION define

MAKE_RESTRAINTS

Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Coordinate files and derivative | Residues with defined topology, | Residues with defined topology, | Block (BLK) residues with | PATCH_SS_TEMPLATES guess | PICK_ATOMS select | Static and dynamic restraints | MAKE_RESTRAINTS make | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | SPLINE_RESTRAINTS approximate | READ_RESTRAINTS read | WRITE_RESTRAINTS write | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | Flowchart of comparative modeling

MAKE_SCHEDULE

MAKE_SCHEDULE create | READ_SCHEDULE read | READ_SCHEDULE read | WRITE_SCHEDULE write | Flowchart of comparative modeling

MAKE_TOPOLOGY_MODEL

READ_TOPOLOGY read | MAKE_TOPOLOGY_MODEL make | WRITE_TOPOLOGY_MODEL write | WRITE_TOPOLOGY_MODEL write

MALIGN

Preparing an initial family | Detailed chronological listing of | ALIGN align | MALIGN align | MALIGN3D align | SEQUENCE_SEARCH search

MALIGN3D

Preparing an initial family | Becoming familiar with the | Detailed chronological listing of | Detailed chronological listing of | Coordinate files and derivative | TRANSFER_XYZ copy | ALIGN align | COMPARE compare | MALIGN3D align | Flowchart of comparative modeling

MATRIX_FILE

ID_TABLE calculate | ID_TABLE calculate | SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare | DENDROGRAM clustering | PRINCIPAL_COMPONENTS clustering | COMPARE compare | COMPARE compare

MATRIX_OFFSET

ALIGN align | ALIGN align | ALIGN align | ALIGN align | ALIGN align | ALIGN align | ALIGN2D align | MALIGN align | ALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search

MAX_GAPS_MATCH

SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare

MAX_ITERATIONS

OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

MAX_LOOP_LENGTH

PICK_ATOMS select | PICK_ATOMS select

MAXIMAL_DISTANCE

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

MD_RETURN

OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

MD_TIME_STEP

OPTIMIZE optimize | OPTIMIZE optimize

MDT_LIB_FILE

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

method

Method for comparative protein

MIN_ATOM_SHIFT

OPTIMIZE optimize

MIN_ATOM_SHIFTS

OPTIMIZE optimize

MIN_LOOP_LENGTH

SEGMENT_MATCHING align | SEGMENT_MATCHING align | SEGMENT_MATCHING align

MNCH?_LIB

Detailed chronological listing of

MNCH_LIB

MAKE_RESTRAINTS make

MODEL2_SEGMENT

READ_MODEL2 read

MODEL_FORMAT

READ_MODEL read | READ_MODEL2 read | WRITE_MODEL write | WRITE_MODEL2 write

MODEL_SEGMENT

READ_MODEL read | READ_MODEL read | READ_MODEL read | WRITE_PDB_XREF write | Alignment file format | Alignment file format | Alignment file format

MODEL_TOPOLOGY

Frequently asked questions (FAQ)

MODELLER_STATUS

Detailed chronological listing of | Controlling breakpoints and the | Controlling breakpoints and the | READ_ALIGNMENT read | READ_ALIGNMENT2 read | ALIGN align | ALIGN align | ALIGN2D align | MALIGN align | ALIGN_CONSENSUS consensus | ALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

MOLPDF

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

MUTATE_MODEL

MUTATE_MODEL mutate | PICK_ATOMS select

N_SCHEDULE

READ_SCHEDULE read

NLOGN_USE

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

NO_TER

Detailed chronological listing of | WRITE_MODEL write

NONBONDED_SEL_ATOMS

Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | PICK_RESTRAINTS pick | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

NORMALIZE

Detailed chronological listing of | Detailed chronological listing of

NORMALIZE_PROFILE

ENERGY evaluate | ENERGY evaluate

NUMBER_LINES

OPEN open | OPEN open

NUMBER_PLACES

TOP Commands | TOP Commands | WRITE write | WRITE write | Predefined TOP variables

OBJECTS

Detailed chronological listing of | WRITE write | WRITE write | Predefined TOP variables

OBJECTS_FILE

OPEN open | Predefined TOP variables

OFF_DIAGONAL

ALIGN align | ALIGN align | ALIGN2D align | MALIGN align | ALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search

OPEN

OPEN open

OPERATE

Detailed chronological listing of | Detailed chronological listing of | OPERATE perform

OPERATION

OPERATE perform | STRING_OPERATE perform | IF conditional | STRING_IF conditional | Predefined TOP variables

OPTIMIZATION_METHOD

OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

OPTIMIZE

Detailed chronological listing of | Detailed chronological listing of | GENERATE_TOPOLOGY generate | PICK_HOT_ATOMS pick | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | PICK_RESTRAINTS pick | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | SWITCH_TRACE open | Flowchart of comparative modeling | Flowchart of comparative modeling | Flowchart of comparative modeling | Flowchart of comparative modeling | Flowchart of comparative modeling | Function

ORIENT_MODEL

ORIENT_MODEL center

OUTPUT

Major changes in Releases | Detailed chronological listing of | Detailed chronological listing of | WRITE_DATA write | WRITE_DATA write | WRITE_DATA write | COMPARE compare | COMPARE compare | ALIGN3D align | ALIGN3D align | ALIGN3D align | ALIGN3D align | MALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | DEFINE_SYMMETRY define | ENERGY evaluate | ENERGY evaluate | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

OUTPUT_CONTROL

Controlling breakpoints and the | Controlling breakpoints and the | Controlling breakpoints and the | Predefined TOP variables

OUTPUT_DIRECTORY

Output. | WRITE_TOPOLOGY_MODEL write | WRITE_MODEL write | WRITE_MODEL2 write | WRITE_PDB_XREF write | SEQUENCE_TO_ALI copy | WRITE_ALIGNMENT write | ID_TABLE calculate | ID_TABLE calculate | SEQUENCE_COMPARISON compare | SEGMENT_MATCHING align | SEGMENT_MATCHING align | WRITE_RESTRAINTS write | WRITE_SCHEDULE write | WRITE write | WRITE_TOP write | Predefined TOP variables

OUTPUT_WEIGHTS_FILE

ALIGN align | ALIGN2D align | ALIGN_CONSENSUS consensus

OVERHANG

WRITE_ALIGNMENT write | WRITE_ALIGNMENT write | ALIGN align | ALIGN align | ALIGN2D align | MALIGN align | ALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search

PATCH

Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | READ_TOPOLOGY read | READ_PARAMETERS read | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH patch | DELETE_ALIGNMENT delete

PATCH_DEFAULT

GENERATE_TOPOLOGY generate | PATCH patch

PATCH_DISULFIDES

Detailed chronological listing of

PATCH_SS_MODEL

Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Detailed chronological listing of | PATCH_SS_MODEL guess

PATCH_SS_TEMPLATES

Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Detailed chronological listing of | PATCH_SS_TEMPLATES guess | PATCH_SS_MODEL guess | Flowchart of comparative modeling

PICK_ATOMS

Frequently asked questions (FAQ) | Frequently asked questions (FAQ) | Detailed chronological listing of | Block (BLK) residues with | MUTATE_MODEL mutate | PICK_ATOMS select | PICK_ATOMS select | SUPERPOSE superpose | MAKE_RESTRAINTS make | OPTIMIZE optimize

PICK_ATOMS_SET

PICK_ATOMS select | PICK_ATOMS select

PICK_HOT_ATOMS

GENERATE_TOPOLOGY generate | PICK_HOT_ATOMS pick | Formats of the restraints | OPTIMIZE optimize | OPTIMIZE optimize | Function

PICK_HOT_CUTOFF

PICK_HOT_ATOMS pick | PICK_HOT_ATOMS pick

PICK_RESTRAINTS

Frequently asked questions (FAQ) | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | PICK_ATOMS select | PICK_HOT_ATOMS pick | DEFINE_SYMMETRY define | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | MAKE_SCHEDULE create | READ_SCHEDULE read | Flowchart of comparative modeling

primer, modeling

Comparative protein modeling primer

PRINCIPAL_COMPONENTS

Selecting the templates | ID_TABLE calculate | PRINCIPAL_COMPONENTS clustering | COMPARE compare

PROBE_RADIUS

WRITE_DATA write

PROFILE_2D_PHYS

Detailed chronological listing of

program distribution

Distribution

program updates

MODELLER updates

PSA_INTEGRATION_STEP

WRITE_DATA write

RADII_FACTOR

WRITE_DATA write | WRITE_DATA write | MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

RAND_SEED

BUILD_MODEL build | RANDOMIZE_XYZ randomize | ROTATE_DIHEDRALS change | ROTATE_DIHEDRALS change | MAKE_REGION define | SEQUENCE_SEARCH search | OPTIMIZE optimize | OPTIMIZE optimize

RANDOMIZE

ROTATE_DIHEDRALS change

RANDOMIZE_XYZ

PICK_ATOMS select | RANDOMIZE_XYZ randomize | MAKE_SCHEDULE create | Flowchart of comparative modeling

READ

READ read

READ_ALIGNMENT

Detailed chronological listing of | READ_ALIGNMENT read | READ_ALIGNMENT2 read | COMPARE_ALIGNMENTS compare | COMPARE_ALIGNMENTS compare | WRITE_ALIGNMENT write | DESCRIBE describe | COMPARE compare | Flowchart of comparative modeling

READ_ALIGNMENT2

Detailed chronological listing of | READ_ALIGNMENT2 read | COMPARE_ALIGNMENTS compare | COMPARE_ALIGNMENTS compare

READ_ATOM_CLASS

READ_ATOM_CLASS read

READ_MODEL

Residues with defined topology, | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_MODEL guess | READ_MODEL read | READ_MODEL2 read | READ_MODEL2 read | WRITE_MODEL write | WRITE_MODEL2 write | BUILD_MODEL build | ROTATE_DIHEDRALS change | CONDENSE_RESTRAINTS remove | Flowchart of comparative modeling

READ_MODEL2

READ_MODEL2 read

READ_PARAMETERS

Detailed chronological listing of | READ_PARAMETERS read

READ_RESTRAINTS

Frequently asked questions (FAQ) | READ_RESTRAINTS read | WRITE_RESTRAINTS write

READ_RESTYP_LIB

Frequently asked questions (FAQ) | Detailed chronological listing of | READ_RESTYP_LIB read

READ_SCHEDULE

MAKE_SCHEDULE create | READ_SCHEDULE read | WRITE_SCHEDULE write

READ_TOPOLOGY

READ_TOPOLOGY read | ROTATE_DIHEDRALS change

READ_WEIGHTS

ALIGN align | ALIGN2D align | ALIGN_CONSENSUS consensus

RECORD

READ read | READ read | Predefined TOP variables

REFERENCE_ATOM

SUPERPOSE superpose | SUPERPOSE superpose | SUPERPOSE superpose

REFERENCE_DISTANCE

SUPERPOSE superpose | SUPERPOSE superpose

REGION_SIZE

MAKE_REGION define

REINDEX_RESTRAINTS

REINDEX_RESTRAINTS renumber

RELATIVE_DIELECTRIC

ENERGY evaluate | OPTIMIZE optimize

REMOVE_GAPS

READ_ALIGNMENT read | READ_ALIGNMENT read | READ_ALIGNMENT2 read | SEQUENCE_SEARCH search

RENAME_SEGMENTS

RENAME_SEGMENTS rename

RENUMBER_RESIDUES

Detailed chronological listing of | RENAME_SEGMENTS rename | RENAME_SEGMENTS rename | RENAME_SEGMENTS rename

RENUMBER_SEGMENTS

Detailed chronological listing of

REORDER_ATOMS

READ_MODEL2 read | REORDER_ATOMS standardize

RES_TYPES

PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select

RESET

RESET reset

RESIDUE_GROUPING

MAKE_RESTRAINTS make

RESIDUE_IDS

Frequently asked questions (FAQ) | PATCH patch | PATCH patch | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

RESIDUE_RANGE

PICK_RESTRAINTS pick | PICK_RESTRAINTS pick

RESIDUE_SPAN_RANGE

Detailed chronological listing of | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

RESIDUE_SPAN_SIGN

Detailed chronological listing of | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | OPTIMIZE optimize

RESIDUE_TYPE

PATCH patch | PATCH patch | MUTATE_MODEL mutate | MUTATE_MODEL mutate

RESTRAINT_PARAMETERS

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | ADD_RESTRAINT add | ADD_RESTRAINT add

RESTRAINT_SEL_ATOMS

Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick

RESTRAINT_STDEV

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

RESTRAINT_TYPE

Block (BLK) residues with | MAKE_RESTRAINTS make | MAKE_RESTRAINTS make | CONDENSE_RESTRAINTS remove

RESTRAINTS_FILTER

PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick | PICK_RESTRAINTS pick

RESTRAINTS_FORMAT

WRITE_RESTRAINTS write

RESTYP_LIB_FILE

Detailed chronological listing of | READ_RESTYP_LIB read | READ_RESTYP_LIB read

RESULT

Detailed chronological listing of | OPERATE perform | OPERATE perform | STRING_OPERATE perform | STRING_OPERATE perform | Predefined TOP variables

RETURN

RETURN return | END_SUBROUTINE end | END_SUBROUTINE end

RMS_CUTOFFS

SUPERPOSE superpose | SUPERPOSE superpose | SUPERPOSE superpose | SUPERPOSE superpose | SUPERPOSE superpose | COMPARE compare | COMPARE compare

ROOT_NAME

Environment variables | Environment variables | EXPAND_ALIGNMENT put | EXPAND_ALIGNMENT put | SEGMENT_MATCHING align | SEGMENT_MATCHING align | SET set | SET set | Predefined TOP variables

ROTATE_DIHEDRALS

PICK_ATOMS select | ROTATE_DIHEDRALS change

ROTATE_MODEL

ROTATE_MODEL rotate

ROTATION_ANGLE

ROTATE_MODEL rotate | ROTATE_MODEL rotate

ROTATION_AXIS

ROTATE_MODEL rotate | ROTATE_MODEL rotate

ROTATION_MATRIX

ROTATE_MODEL rotate | ROTATE_MODEL rotate

ROUTINE

CALL call | CALL call | SUBROUTINE define | Predefined TOP variables

RR_FILE

SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare | ALIGN align | ALIGN align | ALIGN2D align | ALIGN2D align | ALIGN2D align | MALIGN align | MALIGN align | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEGMENT_MATCHING align | SEGMENT_MATCHING align

SCHEDULE_SCALE

MAKE_SCHEDULE create | MAKE_SCHEDULE create | READ_SCHEDULE read | READ_SCHEDULE read

SCHEDULE_STEP

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

script file

Script file | Running MODELLER scripts

SEARCH_CHAINS_FILE

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SEARCH_CHAINS_LIST

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SEARCH_GROUP_LIST

Detailed chronological listing of | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SEARCH_RANDOMIZATIONS

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SEARCH_SORT

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SEARCH_TOP_LIST

SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SEGMENT_CUTOFF

SEGMENT_MATCHING align | SEGMENT_MATCHING align | SEGMENT_MATCHING align | SEGMENT_MATCHING align

SEGMENT_GROWTH_C

SEGMENT_MATCHING align | SEGMENT_MATCHING align | SEGMENT_MATCHING align

SEGMENT_GROWTH_N

SEGMENT_MATCHING align | SEGMENT_MATCHING align | SEGMENT_MATCHING align

SEGMENT_IDS

RENAME_SEGMENTS rename | RENAME_SEGMENTS rename | RENAME_SEGMENTS rename

SEGMENT_MATCHING

Major changes in Releases | Detailed chronological listing of | SEGMENT_MATCHING align

SEGMENT_REPORT

SEGMENT_MATCHING align | SEGMENT_MATCHING align

SEGMENT_SHIFT

SEGMENT_MATCHING align | SEGMENT_MATCHING align

SEGMENT_SHIFTS

SEGMENT_MATCHING align

SELECTION_FROM

PICK_ATOMS select | PICK_ATOMS select

SELECTION_MODE

PICK_ATOMS select | PICK_ATOMS select | PICK_HOT_ATOMS pick | PICK_HOT_ATOMS pick

SELECTION_SEARCH

PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select

SELECTION_SEGMENT

Detailed chronological listing of | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select | Alignment file format

SELECTION_SLAB

PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select

SELECTION_STATUS

PICK_ATOMS select | PICK_ATOMS select

SELECTION_STEP

Detailed chronological listing of

SEQUENCE

GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | ROTATE_DIHEDRALS change

SEQUENCE_COMPARISON

Detailed chronological listing of | ID_TABLE calculate | SEQUENCE_COMPARISON compare | DENDROGRAM clustering | PRINCIPAL_COMPONENTS clustering

SEQUENCE_SEARCH

Finding structures and sequences | Finding structures and sequences | Finding structures and sequences | Detailed chronological listing of | Detailed chronological listing of | SEQUENCE_SEARCH search

SEQUENCE_TO_ALI

MUTATE_MODEL mutate | SEQUENCE_TO_ALI copy

SET

Automatic filename generation | Automatic filename generation | PATCH patch | SET set

SET NLOGN_USE

OPTIMIZE optimize

SHEET_H-BONDS

MAKE_RESTRAINTS make | MAKE_RESTRAINTS make

SIGNIF_CUTOFF

Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | Detailed chronological listing of | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search | SEQUENCE_SEARCH search

SMOOTHING_WINDOW

ENERGY evaluate | ENERGY evaluate | ENERGY evaluate | ENERGY evaluate

SPHERE_CENTER

PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select

SPHERE_RADIUS

PICK_ATOMS select | PICK_ATOMS select | PICK_ATOMS select

SPHERE_STDV

ENERGY evaluate | OPTIMIZE optimize

SPLINE_DX

SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate

SPLINE_MIN_POINTS

SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate

SPLINE_ON_SITE

MAKE_RESTRAINTS make

SPLINE_RANGE

SPLINE_RESTRAINTS approximate

SPLINE_RESTRAINTS

SPLINE_RESTRAINTS approximate

SPLINE_SELECT

SPLINE_RESTRAINTS approximate | SPLINE_RESTRAINTS approximate

STOP

TOP Commands | STOP exit

STOP_ON_ERROR

Controlling breakpoints and the | READ_ALIGNMENT read | READ_ALIGNMENT2 read | ALIGN align | ALIGN2D align | MALIGN align | ALIGN_CONSENSUS consensus | ALIGN3D align | MALIGN3D align | SEQUENCE_SEARCH search | OPTIMIZE optimize | OPTIMIZE optimize | Predefined TOP variables

STRING_ARGUMENTS

STRING_OPERATE perform | STRING_IF conditional | Predefined TOP variables

STRING_IF

STRING_IF conditional

STRING_OPERATE

STRING_OPERATE perform

SUBROUTINE

SUBROUTINE define

SUPERPOSE

Detailed chronological listing of | READ_MODEL2 read | SUPERPOSE superpose | COMPARE compare

SUPERPOSE_REFINE

SUPERPOSE superpose | SUPERPOSE superpose | SUPERPOSE superpose

SWAP_ATOMS_IN_RES

Detailed chronological listing of | SUPERPOSE superpose | SUPERPOSE superpose

SWITCH_TRACE

OPTIMIZE optimize | SWITCH_TRACE open

SYMMETRY_WEIGHT

DEFINE_SYMMETRY define | DEFINE_SYMMETRY define

SYSTEM

SYSTEM execute

TEMPERATURE

OPTIMIZE optimize | OPTIMIZE optimize

templates

Finding structures and sequences | Selecting the templates

THEN

IF conditional | STRING_IF conditional | STRING_IF conditional | Predefined TOP variables

TOPOLOGY_MODEL

READ_TOPOLOGY read | READ_TOPOLOGY read | GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH patch | PATCH_SS_TEMPLATES guess | PATCH_SS_MODEL guess | PATCH_SS_MODEL guess | MAKE_TOPOLOGY_MODEL make | MAKE_TOPOLOGY_MODEL make | MAKE_TOPOLOGY_MODEL make | MAKE_TOPOLOGY_MODEL make | MAKE_TOPOLOGY_MODEL make | WRITE_DATA write | WRITE_DATA write | MAKE_RESTRAINTS make | ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize

TRACE_OUTPUT

OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | SWITCH_TRACE open | SWITCH_TRACE open | SWITCH_TRACE open

TRANSFER_RES_NUMB

READ_MODEL2 read | TRANSFER_RES_NUMB residue

TRANSFER_XYZ

Detailed chronological listing of | Residues with defined topology, | GENERATE_TOPOLOGY generate | BUILD_MODEL build | TRANSFER_XYZ copy | TRANSFER_XYZ copy | MALIGN3D align | Flowchart of comparative modeling

TRANSLATION

ROTATE_MODEL rotate | ROTATE_MODEL rotate

tutorial

Tutorial on using MODELLER

UPDATE_DYNAMIC

ENERGY evaluate | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize | OPTIMIZE optimize

VARIABILITY_FILE

SEQUENCE_COMPARISON compare | SEQUENCE_COMPARISON compare

VARIABLES

DEFINE_INTEGER define | DEFINE_LOGICAL define | DEFINE_REAL define | DEFINE_STRING define | Predefined TOP variables

VIOL_REPORT_CUT

PICK_HOT_ATOMS pick | PICK_HOT_ATOMS pick | ENERGY evaluate | ENERGY evaluate | ENERGY evaluate

VIOL_REPORT_CUT2

ENERGY evaluate | ENERGY evaluate

WATER_IO

GENERATE_TOPOLOGY generate | GENERATE_TOPOLOGY generate | PATCH_SS_TEMPLATES guess | READ_MODEL read | READ_MODEL2 read | TRANSFER_XYZ copy | WRITE_ALIGNMENT write | WRITE_ALIGNMENT write

WRITE

Detailed chronological listing of | WRITE write

WRITE_ALIGNMENT

Detailed chronological listing of | MUTATE_MODEL mutate | WRITE_ALIGNMENT write | ALIGN align | ALIGN2D align | ALIGN_CONSENSUS consensus | MALIGN3D align | SEQUENCE_SEARCH search

WRITE_ALL_ATOMS

WRITE_MODEL write | WRITE_MODEL write

WRITE_DATA

Detailed chronological listing of | WRITE_DATA write | MAKE_REGION define

WRITE_FIT

Becoming familiar with the | MALIGN3D align | MALIGN3D align | MALIGN3D align

WRITE_MODEL

WRITE_MODEL write | Flowchart of comparative modeling | Flowchart of comparative modeling

WRITE_MODEL2

WRITE_MODEL2 write

WRITE_PDB_XREF

WRITE_PDB_XREF write

WRITE_RESTRAINTS

WRITE_RESTRAINTS write | Flowchart of comparative modeling

WRITE_SCHEDULE

MAKE_SCHEDULE create | WRITE_SCHEDULE write

WRITE_TOP

WRITE_TOP write

WRITE_TOPOLOGY_MODEL

WRITE_TOPOLOGY_MODEL write

WRITE_WEIGHTS

ALIGN align | ALIGN2D align | ALIGN_CONSENSUS consensus

WRITE_WHOLE_PDB

MALIGN3D align | MALIGN3D align