Keywords: manual

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## Index

A
  Mathematical forms of restraints
accessibility_type
  model.write_data() write | restraints.make() make
actions
  conjugate_gradients() optimize | molecular_dynamics() optimize | actions.write_structure() write | actions.charmm_trajectory() write
actions.charmm_trajectory()
  automodel.get_optimize_actions() get | model.write_psf() write | actions.charmm_trajectory() write
actions.trace()
  Changes since release 8v2 | automodel.trace_output control | conjugate_gradients() optimize | actions.trace() write | TOP to Python correspondence
actions.write_structure()
  conjugate_gradients() optimize | actions.write_structure() write | actions.charmm_trajectory() write
add
  restraints.add() add | selection.add() add
add_segment
  Changes since release 8v2
align
  alignment.align() align
align2d
  alignment.align2d() align
align3d
  alignment.align3d() align
align3d_repeat
  alignment.align3d() align
align3d_trf
  alignment.align3d() align | Features of proteins used
align_alignment
  alignment.write() write
align_block
  alignment.write() write | alignment.align() align | alignment.malign() align | Alignment of protein sequences | alignment.segment_matching() align
align_codes
  alignment.append() read | alignment.append_model() copy
align_what
  alignment.align() align | Alignment of protein sequences
alignment
  Alignment file | alignment() create
alignment class
  The `alignment` class: comparison
alignment files
  format
    Alignment file (PIR)
  reading
    alignment.append() read
  writing
    alignment.write() write
alignment()
  alignment() create
alignment.align()
  alignment.write() write | alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.consensus() consensus | alignment.align3d() align | alignment.salign() align | Alignment of protein sequences | Alignment of protein structures | TOP to Python correspondence
alignment.align2d()
  Changes since release 8v2 | Coordinate files and derivative | alignment.write() write | alignment.align() align | alignment.align2d() align | alignment.salign() align | Alignment of protein structures | TOP to Python correspondence
alignment.align3d()
  selection.superpose() superpose | alignment.align() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used | TOP to Python correspondence
alignment.append()
  alignment() create | alignment.append() read | alignment.compare_with() compare | alignment.write() write | alignment.describe() describe | profile.build() Build | Flowchart of comparative modeling | TOP to Python correspondence
alignment.append_model()
  selection.mutate() mutate | alignment.append_model() copy | Flowchart of comparative modeling | TOP to Python correspondence
alignment.append_profile()
  alignment.append_profile() add | TOP to Python correspondence
alignment.append_sequence()
  model.build_sequence() build | alignment.append_sequence() add
alignment.check()
  Alignment file | Running MODELLER | Fully automated alignment and | Frequently asked questions (FAQ) | alignment.check() check | Flowchart of comparative modeling | TOP to Python correspondence
alignment.clear()
  alignment.clear() delete
alignment.comments
  alignment.comments alignment
alignment.compare_sequences()
  environ.dendrogram() clustering | environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_sequences() compare | TOP to Python correspondence
alignment.compare_structures()
  Changes since release 9v1 | Changes since release 8v1 | Coordinate files and derivative | environ.dendrogram() clustering | environ.principal_components() clustering | alignment.compare_structures() compare | TOP to Python correspondence
alignment.compare_with()
  alignment.compare_with() compare | alignment.align() align | TOP to Python correspondence
alignment.consensus()
  alignment.write() write | alignment.consensus() consensus | TOP to Python correspondence
alignment.describe()
  alignment.describe() describe | TOP to Python correspondence
alignment.edit()
  alignment.edit() edit | TOP to Python correspondence
alignment.id_table()
  environ.dendrogram() clustering | environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_sequences() compare | TOP to Python correspondence
alignment.malign()
  alignment.align() align | alignment.malign() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used | sequence_db.search() search | TOP to Python correspondence
alignment.malign3d()
  Coordinate files and derivative | model.transfer_xyz() copy | alignment.align() align | alignment.compare_structures() compare | alignment.malign3d() align | alignment.salign() align | Features of proteins used | Flowchart of comparative modeling | TOP to Python correspondence
alignment.salign()
  Changes since release 9v1 | Changes since release 8v1 | alignment.salign() align | Features of proteins used | Alignment of protein structures | Useful SALIGN information and | TOP to Python correspondence
alignment.segment_matching()
  Changes since release 8v0 | alignment.segment_matching() align | TOP to Python correspondence
alignment.to_profile
  environ.make_pssmdb() Create
alignment.to_profile()
  Changes since release 8v2 | alignment.to_profile() convert | profile() create | profile.to_alignment() profile | profile.build() Build | Profile file | TOP to Python correspondence
alignment.write()
  model.make_chains() Fetch | selection.mutate() mutate | alignment.write() write | alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.malign3d() align | profile.build() Build | sequence_db.search() search | TOP to Python correspondence
alignment_features
  alignment.write() write
alignment_format
  model.make_chains() Fetch | alignment.write() write
alignment_type
  Alignment of protein sequences | Alignment of protein structures
allhmodel
  allhmodel() prepare
allhmodel class
  `allhmodel` reference
allhmodel()
  allhmodel() prepare
aln
  automodel.special_restraints() add | model.get_insertions() return | model.get_deletions() return | model.patch_ss_templates() guess | model.transfer_xyz() copy | model.res_num_from() residue | model.color() color | restraints.make() make | selection.superpose() superpose | sequence_db.search() search
aln_base_filename
  profile.scan() Compare
alnfile
  automodel() prepare | loopmodel() prepare
alnseq
  model.generate_topology() generate
alnsequence class
  The `alnsequence` class: a
alnsequence.atom_file
  model.generate_topology() generate | alignment.append_model() copy | alignment.malign3d() align | alnsequence.atom_file PDB | Alignment file (PIR) | TOP to Python correspondence
alnsequence.code
  alignment.append_model() copy | alnsequence.code alignment | Alignment file (PIR) | Profile file | TOP to Python correspondence
alnsequence.get_num_equiv()
  alnsequence.get_num_equiv() get
alnsequence.get_sequence_identity()
  alnsequence.get_sequence_identity() get
alnsequence.name
  alnsequence.name protein
alnsequence.prottyp
  alnsequence.prottyp protein
alnsequence.residues
  alnsequence.residues list
alnsequence.source
  alnsequence.source source
alnsequence.transfer_res_prop()
  alignment.write() write | alnsequence.transfer_res_prop() transfer
alpha
  alpha() make
alpha()
  alpha() make
angular_step_size
  density.grid_search() dock
append
  topology.append() append | parameters.append() append | restraints.append() read | group_restraints.append() read | alignment.append() read
append_model
  alignment.append_model() copy
append_profile
  alignment.append_profile() add
append_sequence
  alignment.append_sequence() add
asgl_output
  selection.energy() evaluate | alignment.compare_structures() compare
assess_dope
  selection.assess_dope() assess
assess_dopehr
  selection.assess_dopehr() assess
assess_ga341
  model.assess_ga341() assess
assess_methods
  Getting a very fast | automodel() prepare
atmsel
  restraints.make() make | restraints.pick() pick
atmsel1
  restraints.make_distance() make
atmsel2
  restraints.make_distance() make
atom class
  The `atom` class: a
atom classes
  Loop modeling method
atom.biso
  atom.biso isotropic
atom.charge
  atom.charge electrostatic
atom.dvx
  atom.dvx objective
atom.mass
  atom.mass mass
atom.name
  atom.name PDB
atom.occ
  atom.occ occupancy
atom.residue
  atom.residue residue
atom.vx
  atom.vx x
atom1
  sheet() make
atom2
  sheet() make
atom_accessibility
  model.make_region() define
atom_files
  alignment.append_model() copy
atom_ids
  Specification of pseudo atoms | restraints.unpick() unselect
atom_range
  model.atom_range() return
auto_align
  automodel.auto_align() generate
auto_overhang
  Alignment of protein structures
automodel
  automodel() prepare
automodel class
  `automodel` reference
automodel()
  Changes since release 8v2 | automodel() prepare | allhmodel() prepare | loopmodel() prepare
automodel.assess_methods
  loopmodel() prepare
automodel.auto_align()
  Fully automated alignment and | automodel.auto_align() generate
automodel.cluster()
  automodel.cluster() cluster
automodel.deviation
  Flowchart of comparative modeling
automodel.ending_model
  Simple usage | automodel.starting_model first | automodel.ending_model last | loopmodel.loop.ending_model last | selection.assess_dope() assess
automodel.final_malign3d
  automodel.final_malign3d final | Flowchart of comparative modeling
automodel.generate_method
  Using your own initial | automodel.generate_method control
automodel.get_model_filename()
  automodel.get_model_filename() get | loopmodel.get_loop_model_filename() get
automodel.get_optimize_actions()
  automodel.trace_output control | automodel.get_optimize_actions() get | automodel.get_refine_actions() get
automodel.get_refine_actions()
  automodel.trace_output control | automodel.get_refine_actions() get
automodel.initial_malign3d
  Building a model from | Changes since release 9v1 | automodel.initial_malign3d initial | model.transfer_xyz() copy
automodel.library_schedule
  Changing the default optimization | automodel() prepare | automodel.library_schedule select | loopmodel.loop.library_schedule select
automodel.make()
  Simple usage | Getting a very fast | Accessing output data after | Fully automated alignment and | automodel.outputs all | automodel.make() build
automodel.max_molpdf
  Changing the default optimization | Changes since release 9v1 | automodel.max_molpdf objective
automodel.max_var_iterations
  Changing the default optimization | automodel.max_var_iterations select | loopmodel.loop.max_var_iterations select
automodel.md_level
  Changing the default optimization | automodel.md_level control | loopmodel.loop.md_level control
automodel.nonstd_restraints()
  Including water molecules, HETATM | automodel.nonstd_restraints() add | Flowchart of comparative modeling
automodel.outputs
  Accessing output data after | automodel.outputs all | loopmodel.loop.outputs all
automodel.rand_method
  Changes since release 9v1 | automodel.rand_method control
automodel.repeat_optimization
  Changing the default optimization | automodel.repeat_optimization number
automodel.select_atoms()
  Refining only part of | automodel.select_atoms() select
automodel.special_patches()
  Including disulfide bridges | Building multi-chain models with | automodel.special_patches() add | Flowchart of comparative modeling
automodel.special_restraints()
  Adding additional restraints to | Building multi-chain models with | automodel.special_restraints() add | Flowchart of comparative modeling
automodel.starting_model
  Simple usage | automodel.starting_model first | automodel.ending_model last | loopmodel.loop.starting_model first
automodel.trace_output
  automodel.trace_output control | automodel.get_optimize_actions() get
automodel.use_parallel_job()
  automodel.use_parallel_job() parallelize
automodel.user_after_single_model()
  Building multi-chain models with | automodel.user_after_single_model() analyze | loopmodel.user_after_single_loop_model() analyze
automodel.very_fast()
  Getting a very fast | automodel.very_fast() request
automodel.write_intermediates
  automodel.write_intermediates write
B
  Mathematical forms of restraints
base_align_codes
  alignment.edit() edit
basis_pdf_weight
  restraints.make() make
basis_relative_weight
  restraints.make() make
best_docked_models
  density.grid_search() dock
bibliography
  MODELLER bibliography
BLOCK residues
  Block (BLK) residues with
breakpoint
  Controlling breakpoints and the
bug reports
  Bug reports
build
  model.build() build | profile.build() Build
build_ini_loop
  loopmodel.build_ini_loop() create
build_method
  model.build() build
build_sequence
  model.build_sequence() build
by_residue
  selection.by_residue() make
cap_atom_shift
  molecular_dynamics() optimize | Molecular dynamics
ccf_func_type
  density.read() read
ccmatrix_offset
  profile.scan() Compare
chains_list
  sequence_db.read() read | sequence_db.write() write
change
  selection.rotate_dihedrals() change
charmm_trajectory
  actions.charmm_trajectory() write
check
  alignment.check() check
check_profile
  profile.build() Build
chop_nonstd_termini
  model.make_chains() Fetch
cispeptide
  cispeptide() creates
cispeptide()
  restraints.add() add | restraints.unpick() unselect | cispeptide() creates
classes
  group_restraints() create | group_restraints.append() read
clean_sequences
  Changes since release 8v2 | sequence_db.read() read
clear
  topology.clear() clear | parameters.clear() clear | restraints.clear() delete | alignment.clear() delete
clear_topology
  model.clear_topology() clear
close_file
  alignment.append() read
cluster
  automodel.cluster() cluster
cluster_cut
  automodel.cluster() cluster | model.transfer_xyz() copy
cluster_method
  model.transfer_xyz() copy
color
  model.color() color
communicator.get_data()
  Parallel job support | job() create | communicator.send_data() send | communicator.get_data() get
communicator.send_data()
  Parallel job support | job() create | job.queue_task() submit | communicator.send_data() send | communicator.get_data() get | slave.run_cmd() run
compactness
  model.assess_ga341() assess
compare_mode
  alignment.compare_structures() compare
compare_sequences
  alignment.compare_sequences() compare
compare_structures
  alignment.compare_structures() compare
compare_with
  alignment.compare_with() compare
complete_pdb
  model.write_psf() write | complete_pdb() read
complete_pdb()
  model.read() read | model.build_sequence() build | selection.assess_dope() assess | complete_pdb() read
condense
  restraints.condense() remove
conjugate_gradients
  conjugate_gradients() optimize
conjugate_gradients()
  Changes since release 8v2 | automodel.max_var_iterations select | Rigid bodies | restraints.make_distance() make | conjugate_gradients() optimize | quasi_newton() optimize | molecular_dynamics() optimize | actions.write_structure() write | actions.trace() write | actions.charmm_trajectory() write | complete_pdb() read | Flowchart of comparative modeling | TOP to Python correspondence
consensus
  alignment.consensus() consensus
contact_shell
  Feature types
convert
  sequence_db.convert() convert
correls
  Mathematical forms of restraints
Coulomb
  Block (BLK) residues with | Static and dynamic restraints | Mathematical forms of restraints | The `energy_data` class: objective | energy_data.contact_shell nonbond | energy_data.dynamic_coulomb calculate | energy_data.coulomb_switch Coulomb | energy_data.relative_dielectric relative | model.read() read | restraints.make() make | restraints.pick() pick | physical.values() create | Function | Coulomb restraint
csrfile
  automodel() prepare
current_directory
  alignment.malign3d() align | Useful SALIGN information and
data_file
  sequence_db.search() search
debug_function
  selection.debug_function() test
debug_function_cutoff
  selection.debug_function() test
default
  modfile.default() generate
delete
  modfile.delete() delete
delta
  Mathematical forms of restraints
dendrogram
  environ.dendrogram() clustering
dendrogram_file
  Alignment of protein structures | Useful SALIGN information and
density
  density() create
density class
  The `density` class: handling
density()
  density() create
density.grid_search()
  The `density` class: handling | density() create | density.read() read | density.grid_search() dock | TOP to Python correspondence
density.read()
  density() create | density.read() read | density.grid_search() dock
density_type
  density.read() read | density.grid_search() dock
describe
  alignment.describe() describe
detailed_debugging
  selection.debug_function() test
deviation
  automodel() prepare | restraints.symmetry.report() report | selection.randomize_xyz() randomize
dih_lib_only
  restraints.make() make
dihedral class
  The `dihedral` class: a
dihedral.atoms
  dihedral.atoms atoms
dihedral.dihclass
  dihedral.dihclass integer
dihedral.value
  dihedral.value current
dihedrals
  selection.rotate_dihedrals() change
distance_rsr_model
  restraints.make_distance() make
disulfide bond restraints
  Including disulfide bridges
dnr_accpt_lib
  model.write_data() write
dope_loopmodel
  dope_loopmodel() prepare
dope_loopmodel class
  `dope_loopmodel` reference
dope_loopmodel()
  Changes since release 8v2 | dope_loopmodel() prepare
dopehr_loopmodel class
  `dopehr_loopmodel` reference
dopehr_loopmodel()
  Changes since release 8v2
dr
  saxsdata.ini_saxs() Initialization
dr_exp
  saxsdata.ini_saxs() Initialization
e_native_comb
  model.assess_ga341() assess
e_native_pair
  model.assess_ga341() assess
e_native_surf
  model.assess_ga341() assess
edat
  Key for command descriptions | environ.edat default | conjugate_gradients() optimize | molecular_dynamics() optimize
edit
  alignment.edit() edit
edit_align_codes
  alignment.edit() edit
edit_file_ext
  alignment.malign3d() align
electrostatics
  see Coulomb
em_fit_output_file
  density.grid_search() dock
em_map_size
  density.read() read
em_pdb_name
  density.grid_search() dock
end
  model.atom_range() return | model.residue_range() return
end_of_file
  alignment.append() read
energy
  selection.energy() evaluate
energy_data
  Key for command descriptions | energy_data() create
energy_data class
  The `energy_data` class: objective
energy_data()
  energy_data() create
energy_data.contact_shell
  energy_data.contact_shell nonbond | energy_data.update_dynamic nonbond | restraints.make() make | conjugate_gradients() optimize | Atomic density | TOP to Python correspondence
energy_data.coulomb_switch
  energy_data.contact_shell nonbond | energy_data.coulomb_switch Coulomb | TOP to Python correspondence
energy_data.covalent_cys
  energy_data.covalent_cys use | TOP to Python correspondence
energy_data.density
  Static and dynamic restraints
energy_data.dynamic_coulomb
  Static and dynamic restraints | energy_data.contact_shell nonbond | energy_data.dynamic_coulomb calculate | restraints.make() make | TOP to Python correspondence
energy_data.dynamic_gbsa
  `dope_loopmodel` reference | Static and dynamic restraints | energy_data.dynamic_gbsa calculate
energy_data.dynamic_lennard
  Static and dynamic restraints | energy_data.contact_shell nonbond | energy_data.dynamic_lennard calculate | restraints.make() make | TOP to Python correspondence
energy_data.dynamic_modeller
  Static and dynamic restraints | energy_data.dynamic_modeller calculate | energy_data.covalent_cys use | model.group_restraints all | The `group_restraints` class: restraints | TOP to Python correspondence
energy_data.dynamic_sphere
  Static and dynamic restraints | energy_data.contact_shell nonbond | energy_data.sphere_stdv soft-sphere | energy_data.dynamic_sphere calculate | restraints.make() make | TOP to Python correspondence
energy_data.energy_terms
  energy_data.energy_terms user-defined | User-defined energy terms
energy_data.excl_local
  energy_data.excl_local exclude | restraints.make_distance() make | TOP to Python correspondence
energy_data.lennard_jones_switch
  energy_data.contact_shell nonbond | energy_data.lennard_jones_switch Lennard-Jones | TOP to Python correspondence
energy_data.nlogn_use
  energy_data.nlogn_use select | conjugate_gradients() optimize | TOP to Python correspondence
energy_data.nonbonded_sel_atoms
  Refining only part of | energy_data.nonbonded_sel_atoms control | restraints.make() make | restraints.pick() pick | TOP to Python correspondence
energy_data.radii_factor
  energy_data.contact_shell nonbond | energy_data.radii_factor scale | model.write_data() write | TOP to Python correspondence
energy_data.relative_dielectric
  energy_data.relative_dielectric relative | Coulomb restraint | TOP to Python correspondence
energy_data.saxsdata
  Static and dynamic restraints
energy_data.solvent_model
  energy_data.solvent_model select
energy_data.sphere_stdv
  energy_data.sphere_stdv soft-sphere | energy_data.dynamic_sphere calculate | TOP to Python correspondence
energy_data.update_dynamic
  energy_data.contact_shell nonbond | energy_data.update_dynamic nonbond | conjugate_gradients() optimize | molecular_dynamics() optimize | TOP to Python correspondence
env.io.hetatm
  Including water molecules, HETATM
env.io.hydrogen
  Including water molecules, HETATM | Building an all hydrogen
env.io.water
  Including water molecules, HETATM
environ
  environ() create
environ class
  The `environ` class: MODELLER
environ()
  Simple usage | Frequently asked questions (FAQ) | environ() create | TOP to Python correspondence
environ.dendrogram()
  environ.dendrogram() clustering | model.transfer_xyz() copy | alignment.id_table() calculate | alignment.compare_structures() compare | sequence_db.search() search | TOP to Python correspondence
environ.edat
  Key for command descriptions | environ.edat default | energy_data() create
environ.io
  Key for command descriptions | environ.io default | io_data() create
environ.libs
  environ.libs MODELLER
environ.make_pssmdb()
  environ.make_pssmdb() Create | profile.scan() Compare
environ.principal_components()
  environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_structures() compare | TOP to Python correspondence
environ.schedule_scale
  Changing the default optimization | environ.schedule_scale energy | schedule() create
environ.system()
  environ.system() execute | TOP to Python correspondence
equilibrate
  molecular_dynamics() optimize | Molecular dynamics
excluded pairs
  Excluded pairs
excluded_atom
  Excluded pairs
exit_stage
  automodel.make() build
ext_tree_file
  Alignments using external restraints
extend_by_residue
  selection.extend_by_residue() extend
extend_hot_spot
  Changes since release 8v2
extension
  model.get_insertions() return | model.get_deletions() return | selection.extend_by_residue() extend
factor
  Mathematical forms of restraints
fast_search
  sequence_db.search() search
fast_search_cutoff
  sequence_db.search() search
feature
  Mathematical forms of restraints | restraints.spline() approximate
feature_weight
  Features of proteins used
feature_weights
  Useful SALIGN information and
features.angle
  Feature types
features.density
  Feature types
features.dihedral
  Feature types
features.dihedral_diff
  Feature types
features.distance
  Feature types
features.minimal_distance
  Feature types
features.solvent_access
  Feature types
features.x_coordinate
  Feature types
features.y_coordinate
  Feature types
features.z_coordinate
  Feature types
fh
  schedule.write() write
file
  environ.principal_components() clustering | topology.append() append | parameters.append() append | model.write_data() write | group_restraints.append() read | alignment.segment_matching() align | density.read() read
file naming
  File naming
file types
  File types
file_exists
  modfile.inquire() check
file_ext
  alignment.segment_matching() align | modfile.default() generate
file_id
  alignment.segment_matching() align | modfile.default() generate
filename
  saxsdata.ini_saxs() Initialization | complete_pdb() read
filepattern
  actions.write_structure() write
filter
  sequence_db.filter() cluster
first
  actions.write_structure() write | actions.charmm_trajectory() write
fit
  selection.superpose() superpose | alignment.write() write | alignment.align2d() align | alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | Features of proteins used | Useful SALIGN information and
fit_atoms
  alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | Features of proteins used
fit_on_first
  Features of proteins used | Useful SALIGN information and
fit_pdbnam
  Features of proteins used
fix_offsets
  Alignments using external restraints
form
  restraints.spline() approximate
forms.cosine
  Mathematical forms of restraints
forms.coulomb
  Mathematical forms of restraints
forms.factor
  Mathematical forms of restraints
forms.gaussian
  Mathematical forms of restraints
forms.lennard_jones
  Mathematical forms of restraints
forms.lower_bound
  Mathematical forms of restraints
forms.multi_binormal
  Mathematical forms of restraints
forms.multi_gaussian
  Mathematical forms of restraints
forms.nd_spline
  Mathematical forms of restraints
forms.spline
  Mathematical forms of restraints
forms.upper_bound
  Mathematical forms of restraints
frequently asked questions
  Frequently asked questions (FAQ)
gap_function
  alignment.salign() align | Alignment of protein sequences | Alignment of protein structures
gap_gap_score
  Gap penalties and correcting
gap_penalties_1d
  alignment.align() align | alignment.align2d() align | alignment.malign() align | Gap penalties and correcting | profile.scan() Compare | sequence_db.search() search | sequence_db.filter() cluster | Profile file
gap_penalties_2d
  Changes since release 8v2 | alignment.align2d() align | Alignment of protein structures | Gap penalties and correcting
gap_penalties_3d
  alignment.align3d() align | alignment.malign3d() align | Features of proteins used | Gap penalties and correcting
gap_residue_score
  Gap penalties and correcting
gaps_in_target
  profile.build() Build
generate_topology
  model.generate_topology() generate
get_data
  communicator.get_data() get
get_deletions
  model.get_deletions() return
get_insertions
  model.get_insertions() return
get_loop_model_filename
  loopmodel.get_loop_model_filename() get
get_model_filename
  automodel.get_model_filename() get
get_num_equiv
  alnsequence.get_num_equiv() get
get_optimize_actions
  automodel.get_optimize_actions() get
get_refine_actions
  automodel.get_refine_actions() get
get_sequence_identity
  alnsequence.get_sequence_identity() get
grid_search
  density.grid_search() dock
group
  restraints.spline() approximate
group_restraints
  group_restraints() create
group_restraints class
  The `group_restraints` class: restraints
group_restraints()
  model.group_restraints all | group_restraints() create | TOP to Python correspondence
group_restraints.append()
  group_restraints() create | group_restraints.append() read | TOP to Python correspondence
guide_factor
  molecular_dynamics() optimize
guide_time
  molecular_dynamics() optimize
high
  Mathematical forms of restraints
highderiv
  Mathematical forms of restraints
host
  job() create
hot_atoms
  selection.hot_atoms() atoms
id1
  modfile.default() generate
id2
  modfile.default() generate
id_table
  alignment.id_table() calculate
improve_alignment
  Features of proteins used | Useful SALIGN information and
info.bindir
  info.bindir return
info.build_date
  info.version return | info.build_date return
info.debug
  info.debug returns
info.exe_type
  info.exe_type return
info.time_mark()
  info.time_mark() print | TOP to Python correspondence
info.version
  info.version return
info.version_info
  info.version return | info.version_info return
ini_saxs
  saxsdata.ini_saxs() Initialization
inifile
  Changes since release 8v2 | automodel() prepare
inimodel
  loopmodel() prepare
init_velocities
  molecular_dynamics() optimize
initialize_xyz
  model.build() build
input_weights_file
  Features of proteins used
inquire
  modfile.inquire() check
installation
  Obtaining and installing the
intersegment
  restraints.make() make
io
  Key for command descriptions | environ.io default | model.generate_topology() generate | alignment.append() read | alignment.edit() edit
io_data
  io_data() create
io_data class
  The `io_data` class: coordinate
io_data()
  Key for command descriptions | io_data() create
io_data.atom_files_directory
  Simple usage | Coordinate files and derivative | io_data.atom_files_directory search | TOP to Python correspondence
io_data.hetatm
  Block (BLK) residues with | io_data() create | io_data.hetatm whether | TOP to Python correspondence
io_data.hydrogen
  io_data() create | io_data.hydrogen whether | TOP to Python correspondence
io_data.water
  io_data() create | io_data.water whether | TOP to Python correspondence
job
  job() create
job class
  Parallel job support
job()
  job() create | sge_pe_job() create | sge_qsub_job() create
job.queue_task()
  Parallel job support | job() create | job.queue_task() submit
job.run_all_tasks()
  Parallel job support | job() create | job.queue_task() submit | job.run_all_tasks() run
job.start()
  Parallel job support | job() create | job.start() start
knowns
  Building a model from | automodel() prepare | loopmodel() prepare
last
  actions.write_structure() write | actions.charmm_trajectory() write
last_scales
  schedule() create | schedule.make_for_model() trim
Lennard-Jones
  Frequently asked questions (FAQ) | `dope_loopmodel` reference | Residues with defined topology, | Block (BLK) residues with | Static and dynamic restraints | Mathematical forms of restraints | energy_data.contact_shell nonbond | energy_data.dynamic_lennard calculate | energy_data.lennard_jones_switch Lennard-Jones | restraints.make() make | restraints.pick() pick | selection.assess_dope() assess | physical.values() create | Function | Lennard-Jones restraint
level
  log.level() Set
libraries.parameters
  libraries.parameters parameter
libraries.topology
  libraries.topology topology
library_schedule
  Changes since release 8v2 | automodel() prepare
local_alignment
  alignment.align() align | alignment.salign() align
local_slave
  local_slave() create
local_slave()
  local_slave() create
log object
  The `log` object: controlling
log.level()
  log.level() Set | TOP to Python correspondence
log.minimal()
  log.minimal() display
log.none()
  log.none() display
log.verbose()
  Useful SALIGN information and | log.verbose() display
log.very_verbose()
  log.very_verbose() display
loop modeling
  Loop optimization | Loop modeling method
loop_assess_methods
  loopmodel() prepare
loopmodel
  loopmodel() prepare
loopmodel class
  `loopmodel` reference
loopmodel()
  loopmodel() prepare | dope_loopmodel() prepare
loopmodel.build_ini_loop()
  Changes since release 9v1 | Changes since release 8v2 | loopmodel.build_ini_loop() create
loopmodel.get_loop_model_filename()
  automodel.get_model_filename() get | loopmodel.get_loop_model_filename() get
loopmodel.loop.assess_methods
  automodel() prepare
loopmodel.loop.ending_model
  Automatic loop refinement after | loopmodel.loop.ending_model last | Loop modeling method
loopmodel.loop.library_schedule
  Changes since release 9v1 | loopmodel.loop.library_schedule select
loopmodel.loop.max_var_iterations
  Changes since release 9v1 | loopmodel.loop.max_var_iterations select
loopmodel.loop.md_level
  loopmodel.loop.md_level control
loopmodel.loop.outputs
  Accessing output data after | loopmodel.loop.outputs all
loopmodel.loop.starting_model
  Automatic loop refinement after | loopmodel.loop.starting_model first | Loop modeling method
loopmodel.read_potential()
  loopmodel.read_potential() read
loopmodel.select_loop_atoms()
  Defining loop regions for | Refining an existing PDB | loopmodel.select_loop_atoms() select | Loop modeling method
loopmodel.user_after_single_loop_model()
  Changes since release 9v1 | loopmodel.user_after_single_loop_model() analyze
loops
  model.loops() return
low
  Mathematical forms of restraints
lowderiv
  Mathematical forms of restraints
make
  automodel.make() build | topology.make() make | restraints.make() make
make_chains
  model.make_chains() Fetch
make_distance
  restraints.make_distance() make
make_for_model
  schedule.make_for_model() trim
make_pssmdb
  environ.make_pssmdb() Create
make_region
  model.make_region() define
malign
  alignment.malign() align
malign3d
  alignment.malign3d() align
matrix_comparison
  Alignment of protein sequences
matrix_file
  alignment.id_table() calculate | alignment.compare_sequences() compare | alignment.compare_structures() compare
matrix_offset
  environ.make_pssmdb() Create | alignment.align() align | profile.scan() Compare | sequence_db.filter() cluster | Profile file
matrix_offset_3d
  Changes since release 8v1 | Features of proteins used
max_aln_evalue
  profile.scan() Compare | profile.build() Build
max_atom_shift
  quasi_newton() optimize
max_diff_res
  sequence_db.filter() cluster
max_gaps_match
  alignment.compare_sequences() compare
max_iterations
  automodel.max_var_iterations select | conjugate_gradients() optimize | molecular_dynamics() optimize
max_nonstdres
  model.make_chains() Fetch
max_unaligned_res
  sequence_db.filter() cluster
maximal_distance
  restraints.make_distance() make
maxlength
  model.get_insertions() return
maxs
  saxsdata.ini_saxs() Initialization
maxslave
  sge_qsub_job() create
md_return
  molecular_dynamics() optimize
md_time_step
  molecular_dynamics() optimize
mdl
  model.res_num_from() residue | model.orient() center | restraints.reindex() renumber | selection.superpose() superpose | schedule.make_for_model() trim | alignment.append_model() copy | alignment.compare_sequences() compare | complete_pdb() read
mean
  Mathematical forms of restraints
means
  Mathematical forms of restraints
memory
  log.level() Set
method
  Method for comparative protein
min_atom_shift
  conjugate_gradients() optimize
min_base_entries
  alignment.edit() edit
min_loop_length
  alignment.segment_matching() align
minimal
  log.minimal() display
minimal_chain_length
  model.make_chains() Fetch
minimal_resolution
  model.make_chains() Fetch
minimal_stdres
  model.make_chains() Fetch
minlength
  model.get_insertions() return
minmax_db_seq_len
  sequence_db.read() read
missing parameters
  Frequently asked questions (FAQ) | Residues with defined topology,
mixflag
  saxsdata.ini_saxs() Initialization
model
  model() create
model class
  The `model` class: handling
model()
  model() create
model.assess_ga341()
  automodel() prepare | model.seq_id sequence | model.assess_ga341() assess | selection.assess_dope() assess
model.atom_range()
  Feature types | model.atoms all | model.atom_range() return | The `selection` class: handling
model.atoms
  Feature types | model.atoms all | model.atom_range() return | The `selection` class: handling | The `atom` class: a
model.build()
  Residues with defined topology, | model.remark text | model.build_sequence() build | model.generate_topology() generate | model.build() build | model.transfer_xyz() copy | Flowchart of comparative modeling | TOP to Python correspondence
model.build_sequence()
  model.build_sequence() build | alignment.append_sequence() add
model.chains
  model.chains all | The `selection` class: handling
model.clear_topology()
  Changes since release 8v2 | model.clear_topology() clear | model.generate_topology() generate
model.color()
  model.color() color | TOP to Python correspondence
model.generate_topology()
  Frequently asked questions (FAQ) | Changes since release 8v2 | model.read() read | model.clear_topology() clear | model.generate_topology() generate | model.write_psf() write | model.patch() patch | model.patch_ss_templates() guess | restraints.make() make | selection.rotate_dihedrals() change | Flowchart of comparative modeling | TOP to Python correspondence
model.get_deletions()
  model.get_insertions() return | model.get_deletions() return | model.loops() return | The `selection` class: handling
model.get_insertions()
  model.get_insertions() return | model.get_deletions() return | model.loops() return | The `selection` class: handling
model.group_restraints
  energy_data.dynamic_modeller calculate | model.group_restraints all
model.last_energy
  model.last_energy last
model.loops()
  model.get_insertions() return | model.get_deletions() return | model.loops() return | The `selection` class: handling
model.make_chains()
  model.make_chains() Fetch | TOP to Python correspondence
model.make_region()
  model.make_region() define | TOP to Python correspondence
model.orient()
  model.orient() center | TOP to Python correspondence
model.patch()
  Including disulfide bridges | Frequently asked questions (FAQ) | Changes since release 9v1 | topology.append() append | parameters.append() append | model.generate_topology() generate | model.patch() patch | TOP to Python correspondence
model.patch_ss()
  model.patch_ss() guess | TOP to Python correspondence
model.patch_ss_templates()
  Including disulfide bridges | model.patch_ss_templates() guess | model.patch_ss() guess | Flowchart of comparative modeling | TOP to Python correspondence
model.point()
  model.point() return | The `point` class: a
model.read()
  Changes since release 8v2 | Residues with defined topology, | model() create | model.read() read | model.write() write | model.generate_topology() generate | model.patch_ss() guess | model.build() build | model.make_chains() Fetch | restraints.condense() remove | selection.rotate_dihedrals() change | complete_pdb() read | Flowchart of comparative modeling | TOP to Python correspondence
model.remark
  model.remark text
model.rename_segments()
  Building multi-chain models with | model.rename_segments() rename | TOP to Python correspondence
model.reorder_atoms()
  model.reorder_atoms() standardize | TOP to Python correspondence
model.res_num_from()
  model.generate_topology() generate | model.res_num_from() residue | TOP to Python correspondence
model.residue_range()
  Refining only part of | Feature types | model.residues all | model.residue_range() return | alpha() make | strand() make | The `selection` class: handling
model.residues
  Feature types | model.residues all | model.residue_range() return | The `selection` class: handling | The `residue` class: a
model.resolution
  model.resolution resolution
model.restraints
  model.restraints all | The `restraints` class: static
model.saxs_chifun()
  model.saxs_chifun() Calculate
model.saxs_intens()
  model.saxs_intens() Calculate
model.saxs_pr()
  model.saxs_pr() Calculate | saxsdata.saxs_pr_read() Read
model.seq_id
  model.seq_id sequence | model.assess_ga341() assess
model.to_iupac()
  model() create | model.to_iupac() standardize | TOP to Python correspondence
model.transfer_xyz()
  automodel.cluster() cluster | Residues with defined topology, | environ.dendrogram() clustering | model.seq_id sequence | model.generate_topology() generate | model.build() build | model.transfer_xyz() copy | alignment.malign3d() align | Flowchart of comparative modeling | TOP to Python correspondence
model.write()
  model.write() write | model.write_data() write | model.make_region() define | model.color() color | selection.write() write | Flowchart of comparative modeling | TOP to Python correspondence
model.write_data()
  energy_data.radii_factor scale | model.write() write | model.write_data() write | model.make_region() define | atom.biso isotropic | TOP to Python correspondence
model.write_psf()
  model.write_psf() write | actions.charmm_trajectory() write
model_segment
  Changes since release 8v2 | Changes since release 8v1 | model.read() read | complete_pdb() read | Alignment file (PIR)
modeller_path
  job() create
modfile.default()
  modfile.default() generate
modfile.delete()
  modfile.delete() delete | TOP to Python correspondence
modfile.inquire()
  modfile.inquire() check | TOP to Python correspondence
molecular_dynamics
  molecular_dynamics() optimize
molecular_dynamics()
  Changes since release 8v2 | molecular_dynamics() optimize | actions.write_structure() write | actions.charmm_trajectory() write | Flowchart of comparative modeling | TOP to Python correspondence
molpdf
  selection.energy() evaluate | selection.assess_dope() assess | selection.assess_dopehr() assess | conjugate_gradients() optimize | quasi_newton() optimize | molecular_dynamics() optimize
mutate
  selection.mutate() mutate
n_prof_iterations
  profile.build() Build | Profile file
n_subopt
  Sub-optimal alignments
natomtyp
  saxsdata.ini_saxs() Initialization
nd_spline.add_dimension
  Mathematical forms of restraints
neighbor_cutoff
  model.write_data() write
nmesh
  saxsdata.ini_saxs() Initialization
nodename
  sge_pe_slave() create | ssh_slave() create
none
  log.none() display
nonstd_restraints
  automodel.nonstd_restraints() add
normalize_pp_scores
  Useful SALIGN information and
normalize_profile
  selection.energy() evaluate
nr
  saxsdata.ini_saxs() Initialization
nr_exp
  saxsdata.ini_saxs() Initialization
nsegm
  Changes since release 8v1
number_of_steps
  density.grid_search() dock
obj
  selection.add() add
off_diagonal
  alignment.align() align
only_atom_types
  selection.only_atom_types() select
only_het_residues
  selection.only_het_residues() select
only_mainchain
  selection.only_mainchain() select
only_no_topology
  selection.only_no_topology() select
only_residue_types
  selection.only_residue_types() select
only_sidechain
  selection.only_sidechain() select
only_std_residues
  selection.only_std_residues() select
open
  Mathematical forms of restraints
optimization
  conjugate gradients
    conjugate_gradients() optimize
  molecular dynamics
    molecular_dynamics() optimize
  quasi-Newton
    quasi_newton() optimize
  user-defined
    User-defined optimizers
  variable target function method
    schedule() create
options
  sge_qsub_job() create
orient
  model.orient() center
orient_data
  model.orient() center
outfile
  sequence_db.convert() convert
output
  model.write_data() write | restraints.spline() approximate | selection.energy() evaluate | conjugate_gradients() optimize | actions.trace() write | alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Useful SALIGN information and | sequence_db.search() search
output_alignments
  profile.scan() Compare
output_cod_file
  sequence_db.filter() cluster
output_grp_file
  sequence_db.filter() cluster
output_score_file
  profile.scan() Compare | profile.build() Build
output_weights_file
  Useful SALIGN information and
overhang
  alignment.edit() edit | alignment.align() align | Alignment of protein structures
overhang_auto_limit
  Alignment of protein structures
overhang_factor
  Alignment of protein structures
parameters
  group_restraints() create
parameters.append()
  libraries.parameters parameter | parameters.append() append | parameters.read() read
parameters.clear()
  parameters.clear() clear | parameters.read() read
parameters.read()
  automodel() prepare | parameters.read() read | TOP to Python correspondence
patch
  model.patch() patch
patch_default
  model.build_sequence() build | model.generate_topology() generate | model.patch() patch | complete_pdb() read
patch_ss
  model.patch_ss() guess
patch_ss_templates
  model.patch_ss_templates() guess
PDB files
  in alignment files
    Alignment file (PIR)
  reading
    model.read() read
  search path
    io_data.atom_files_directory search
  temperature factor
    model.write() write | model.write_data() write | model.make_region() define | model.color() color | selection.energy() evaluate | alignment.compare_sequences() compare | atom.biso isotropic
  writing
    model.write() write
physical.values class
  physical.values() create
physical.values()
  environ.schedule_scale energy | physical.values() create
pick
  restraints.pick() pick
pick_hot_cutoff
  selection.hot_atoms() atoms
PIR format
  Alignment file (PIR)
point
  model.point() return
point class
  The `point` class: a
point.select_sphere()
  The `selection` class: handling | selection.select_sphere() select | point.select_sphere() select | The `atom` class: a
point.x
  point.x x | The `atom` class: a
pr_smooth
  saxsdata.ini_saxs() Initialization
prf
  alignment.append_profile() add
principal_components
  environ.principal_components() clustering
probe_radius
  model.write_data() write
profile
  profile() create
profile class
  The `profile` class: using
profile()
  profile() create
profile.build()
  environ.make_pssmdb() Create | The `profile` class: using | profile.scan() Compare | profile.build() Build | The `sequence_db` class: using | sequence_db.read() read | sequence_db.write() write | Profile file | TOP to Python correspondence
profile.read()
  Changes since release 8v2 | environ.make_pssmdb() Create | alignment.to_profile() convert | profile() create | profile.read() read | profile.to_alignment() profile | profile.scan() Compare | profile.build() Build | sequence_db.read() read | Profile file | TOP to Python correspondence
profile.scan()
  Changes since release 9v1 | Changes since release 8v2 | environ.make_pssmdb() Create | The `profile` class: using | profile() create | profile.scan() Compare | pssmdb() create | pssmdb.read() read | TOP to Python correspondence
profile.to_alignment()
  alignment.append_profile() add | profile.to_alignment() profile | profile.build() Build | TOP to Python correspondence
profile.write()
  Changes since release 8v2 | profile.write() write | profile.build() Build | TOP to Python correspondence
profile_format
  environ.make_pssmdb() Create | profile.scan() Compare
profile_list_file
  environ.make_pssmdb() Create | profile.scan() Compare
program updates
  MODELLER updates
psa_integration_step
  model.write_data() write
pseudo atoms
  Specification of pseudo atoms
pseudo_atom.ch2
  Specification of pseudo atoms
pseudo_atom.ch31
  Specification of pseudo atoms
pseudo_atom.ch32
  Specification of pseudo atoms
pseudo_atom.gravity_center
  Specification of pseudo atoms
PSF files
  writing
    model.write_psf() write
pssmdb
  pssmdb() create
pssmdb()
  pssmdb() create
pssmdb.read()
  pssmdb() create | pssmdb.read() read
pssmdb_name
  environ.make_pssmdb() Create
Python
  installation
    Obtaining and installing the
  license
    Copyright notice
  used by MODELLER
    Script file
  using MODELLER as a Python module
    Running MODELLER
q1
  Mathematical forms of restraints
q2
  Mathematical forms of restraints
quasi_newton
  quasi_newton() optimize
quasi_newton()
  Changes since release 8v2 | Rigid bodies | quasi_newton() optimize
queue_task
  job.queue_task() submit
rand_seed
  environ() create
randomize_xyz
  selection.randomize_xyz() randomize
read
  topology.read() read | parameters.read() read | model.read() read | profile.read() read | pssmdb.read() read | sequence_db.read() read | density.read() read
read_potential
  loopmodel.read_potential() read
reference_atom
  selection.superpose() superpose
reference_distance
  selection.superpose() superpose
region_size
  model.make_region() define
reindex
  restraints.reindex() renumber
remove_gaps
  alignment.append() read
remove_unpicked
  restraints.remove_unpicked() remove
rename_segments
  model.rename_segments() rename
renumber_residues
  model.rename_segments() rename
reorder_atoms
  model.reorder_atoms() standardize
report
  restraints.symmetry.report() report
represtyp
  saxsdata.ini_saxs() Initialization
res_num_from
  model.res_num_from() residue
residue class
  The `residue` class: a
residue.alpha
  residue.alpha
residue.chi1
  residue.chi1
residue.chi2
  residue.chi2
residue.chi3
  residue.chi3
residue.chi4
  residue.chi4
residue.chi5
  residue.chi5
residue.code
  residue.code One-letter
residue.hetatm
  residue.hetatm HETATM
residue.index
  residue.index internal
residue.name
  residue.name internal
residue.omega
  residue.omega
residue.pdb_name
  residue.pdb_name PDB
residue.phi
  residue.phi | residue.psi | residue.omega | residue.alpha | residue.chi1 | residue.chi2 | residue.chi3 | residue.chi4 | residue.chi5 | The `dihedral` class: a
residue.psi
  residue.psi
residue_grouping
  restraints.make() make
residue_range
  model.residue_range() return
residue_span_range
  Changes since release 8v0 | energy_data.covalent_cys use | restraints.make() make | restraints.pick() pick | conjugate_gradients() optimize
residue_span_sign
  restraints.make() make
residue_type
  model.patch() patch | selection.mutate() mutate
residues
  Frequently asked questions (FAQ) | model.patch() patch | alpha() make | strand() make
resolution
  density.read() read
restraint_group
  restraints.make() make
restraint_sel_atoms
  restraints.make() make | restraints.pick() pick
restraint_stdev
  restraints.make_distance() make
restraint_stdev2
  restraints.make_distance() make
restraint_type
  Block (BLK) residues with | restraints.make() make | restraints.unpick_redundant() unselected
restraints
  feature types
    Feature types
  mathematical forms
    Mathematical forms of restraints
  pseudo atoms
    Specification of pseudo atoms
  rigid bodies
    Rigid bodies
  static versus dynamic
    Static and dynamic restraints
  symmetry
    Symmetry restraints
  violations
    Restraint violations
restraints class
  The `restraints` class: static
restraints.add()
  Frequently asked questions (FAQ) | Static and dynamic restraints | restraints.make() make | restraints.add() add | restraints.unpick() unselect | alpha() make | strand() make | sheet() make | cispeptide() creates | TOP to Python correspondence
restraints.append()
  Frequently asked questions (FAQ) | restraints.append() read | restraints.write() write | TOP to Python correspondence
restraints.clear()
  restraints.pseudo_atoms all | restraints.clear() delete | restraints.append() read
restraints.condense()
  Frequently asked questions (FAQ) | restraints.unpick_redundant() unselected | restraints.remove_unpicked() remove | restraints.condense() remove | restraints.unpick() unselect | restraints.reindex() renumber | TOP to Python correspondence
restraints.excluded_pairs
  Excluded pairs | restraints.excluded_pairs all
restraints.make()
  Frequently asked questions (FAQ) | Changes since release 8v2 | Coordinate files and derivative | Residues with defined topology, | Block (BLK) residues with | Static and dynamic restraints | model.patch_ss_templates() guess | restraints.make() make | restraints.make_distance() make | restraints.pick() pick | restraints.spline() approximate | restraints.append() read | restraints.write() write | Flowchart of comparative modeling | TOP to Python correspondence
restraints.make_distance()
  Frequently asked questions (FAQ) | Changes since release 8v2 | restraints.make() make | restraints.make_distance() make
restraints.pick()
  Frequently asked questions (FAQ) | Changes since release 8v2 | Changes since release 8v0 | restraints.pick() pick | selection.hot_atoms() atoms | schedule() create | Flowchart of comparative modeling | TOP to Python correspondence
restraints.pseudo_atoms
  Specification of pseudo atoms | restraints.pseudo_atoms all
restraints.reindex()
  restraints.reindex() renumber | TOP to Python correspondence
restraints.remove_unpicked()
  restraints.pick() pick | restraints.remove_unpicked() remove | restraints.condense() remove
restraints.rigid_bodies
  Rigid bodies | restraints.rigid_bodies all
restraints.spline()
  Changes since release 9v1 | restraints.make() make | restraints.spline() approximate | TOP to Python correspondence
restraints.symmetry
  Symmetry restraints | restraints.symmetry all
restraints.symmetry.report()
  restraints.symmetry.report() report
restraints.unpick()
  Frequently asked questions (FAQ) | Changes since release 8v2 | restraints.unpick() unselect | TOP to Python correspondence
restraints.unpick_all()
  restraints.unpick_all() unselect | restraints.pick() pick
restraints.unpick_redundant()
  restraints.make() make | restraints.unpick_redundant() unselected | restraints.condense() remove
restraints.write()
  restraints.write() write | Flowchart of comparative modeling | TOP to Python correspondence
restraints_filter
  restraints.pick() pick
restyp_lib_file
  Changes since release 8v0 | environ() create
rewind_file
  alignment.append() read
rho_solv
  saxsdata.ini_saxs() Initialization
rigid bodies
  Rigid bodies
rigid_body
  Rigid bodies
rms_cutoff
  Changes since release 9v1 | selection.superpose() superpose | Useful SALIGN information and
rms_cutoffs
  alignment.compare_structures() compare
root_name
  alignment.segment_matching() align | modfile.default() generate
rotate_dihedrals
  selection.rotate_dihedrals() change
rotate_mass_center
  selection.rotate_mass_center() rotate
rotate_origin
  selection.rotate_origin() rotate
rr_file
  environ.make_pssmdb() Create | alignment.compare_sequences() compare | alignment.align() align | alignment.align2d() align | alignment.malign() align | Features of proteins used | Useful SALIGN information and | alignment.segment_matching() align | profile.scan() Compare | sequence_db.search() search | sequence_db.filter() cluster | Profile file
run_all_tasks
  job.run_all_tasks() run
run_cmd
  slave.run_cmd() run
s_hi
  saxsdata.ini_saxs() Initialization
s_hybrid
  saxsdata.ini_saxs() Initialization
s_low
  saxsdata.ini_saxs() Initialization
s_max
  saxsdata.ini_saxs() Initialization
s_min
  saxsdata.ini_saxs() Initialization
salign
  alignment.salign() align
salign_data
  alignment.salign() align
saxs_chifun
  model.saxs_chifun() Calculate
saxs_intens
  model.saxs_intens() Calculate
saxs_pr
  model.saxs_pr() Calculate
saxs_pr_read
  saxsdata.saxs_pr_read() Read
saxs_read
  saxsdata.saxs_read() Read
saxsdata
  saxsdata() create
saxsdata class
  The `saxsdata` class: using
saxsdata()
  saxsdata() create
saxsdata.ini_saxs()
  saxsdata() create | saxsdata.ini_saxs() Initialization | saxsdata.saxs_read() Read
saxsdata.saxs_pr_read()
  saxsdata.saxs_pr_read() Read
saxsdata.saxs_read()
  saxsdata.saxs_read() Read
scale_factor
  Rigid bodies
scan
  profile.scan() Compare
schedule
  schedule() create
schedule class
  The `schedule` class: variable
schedule()
  Changes since release 8v2 | schedule() create | schedule.make_for_model() trim | schedule.write() write
schedule.make_for_model()
  schedule() create | schedule.make_for_model() trim | TOP to Python correspondence
schedule.write()
  schedule.write() write | TOP to Python correspondence
schedule_scale
  selection.hot_atoms() atoms | selection.energy() evaluate | selection.debug_function() test | selection.assess_dope() assess | conjugate_gradients() optimize
score
  model.assess_ga341() assess
score_statistics
  profile.scan() Compare
script file
  Script file
search
  sequence_db.search() search
search_group_list
  sequence_db.search() search
search_randomizations
  sequence_db.search() search
search_sort
  sequence_db.search() search
search_top_list
  sequence_db.search() search
segment_cutoff
  alignment.segment_matching() align
segment_growth_c
  alignment.segment_matching() align
segment_growth_n
  alignment.segment_matching() align
segment_ids
  model.rename_segments() rename
segment_matching
  alignment.segment_matching() align
segment_report
  alignment.segment_matching() align
segment_shift
  alignment.segment_matching() align
select_atoms
  automodel.select_atoms() select
select_loop_atoms
  loopmodel.select_loop_atoms() select
select_sphere
  selection.select_sphere() select | point.select_sphere() select
selection
  selection() create | selection.hot_atoms() atoms
selection class
  The `selection` class: handling
selection()
  Refining only part of | model.point() return | model.get_insertions() return | model.get_deletions() return | model.loops() return | The `selection` class: handling | selection() create | selection.select_sphere() select | selection.only_atom_types() select | selection.only_residue_types() select | selection.translate() translate | selection.rotate_origin() rotate | selection.rotate_mass_center() rotate | point.select_sphere() select
selection.add()
  The `selection` class: handling | selection.add() add
selection.assess_dope()
  Changes since release 8v2 | automodel() prepare | `dope_loopmodel` reference | model.chains all | selection.assess_dope() assess | selection.assess_dopehr() assess
selection.assess_dopehr()
  Changes since release 8v2 | automodel() prepare | `dopehr_loopmodel` reference | selection.assess_dopehr() assess
selection.by_residue()
  The `selection` class: handling | selection.by_residue() make
selection.debug_function()
  Changes since release 8v2 | selection.debug_function() test | physical.values() create | TOP to Python correspondence
selection.energy()
  Including disulfide bridges | Frequently asked questions (FAQ) | Changes since release 8v2 | Static and dynamic restraints | Mathematical forms of restraints | model.write() write | model.generate_topology() generate | selection.energy() evaluate | selection.debug_function() test | selection.assess_dope() assess | atom.biso isotropic | complete_pdb() read | Function | Flowchart of comparative modeling | TOP to Python correspondence
selection.extend_by_residue()
  Changes since release 8v2 | selection.extend_by_residue() extend | selection.hot_atoms() atoms
selection.hot_atoms()
  Changes since release 8v2 | model.generate_topology() generate | selection.hot_atoms() atoms | Function | TOP to Python correspondence
selection.mutate()
  Changes since release 8v2 | selection.mutate() mutate | TOP to Python correspondence
selection.only_atom_types()
  The `selection` class: handling | selection.only_atom_types() select
selection.only_het_residues()
  The `selection` class: handling | selection.only_het_residues() select
selection.only_mainchain()
  The `selection` class: handling | selection.only_mainchain() select | selection.only_sidechain() select
selection.only_no_topology()
  The `selection` class: handling | selection.only_no_topology() select
selection.only_residue_types()
  The `selection` class: handling | selection.only_residue_types() select
selection.only_sidechain()
  The `selection` class: handling | selection.only_sidechain() select
selection.only_std_residues()
  The `selection` class: handling | selection.only_std_residues() select
selection.randomize_xyz()
  Changes since release 8v2 | selection.randomize_xyz() randomize | schedule() create | Flowchart of comparative modeling | TOP to Python correspondence
selection.rotate_dihedrals()
  Changes since release 8v2 | selection.rotate_dihedrals() change | TOP to Python correspondence
selection.rotate_mass_center()
  selection.rotate_origin() rotate | selection.rotate_mass_center() rotate
selection.rotate_origin()
  Changes since release 8v2 | selection.rotate_origin() rotate | selection.rotate_mass_center() rotate | TOP to Python correspondence
selection.select_sphere()
  The `selection` class: handling | selection.select_sphere() select | point.select_sphere() select
selection.superpose()
  Changes since release 9v1 | Changes since release 8v2 | selection.superpose() superpose | alignment.compare_structures() compare | TOP to Python correspondence
selection.transform()
  Changes since release 8v2 | selection.rotate_origin() rotate | selection.rotate_mass_center() rotate | selection.transform() transform | TOP to Python correspondence
selection.translate()
  Changes since release 8v2 | selection.translate() translate | TOP to Python correspondence
selection.unbuild()
  Changes since release 8v2 | selection.unbuild() undefine | TOP to Python correspondence
selection.write()
  model.write() write | selection.write() write
selection_mode
  Changes since release 8v2
selection_segment
  Alignment file (PIR)
send_data
  communicator.send_data() send
seq
  alnsequence.get_num_equiv() get | alnsequence.get_sequence_identity() get
seq_database_file
  sequence_db.read() read | sequence_db.search() search
seq_database_format
  sequence_db.filter() cluster
seqid_cut
  sequence_db.filter() cluster
sequence
  automodel() prepare | loopmodel() prepare | selection.rotate_dihedrals() change
sequence_db
  sequence_db() create
sequence_db class
  The `sequence_db` class: using
sequence_db()
  sequence_db() create
sequence_db.convert()
  Changes since release 8v2 | sequence_db.read() read | sequence_db.convert() convert
sequence_db.filter()
  Changes since release 8v2 | The `sequence_db` class: using | sequence_db() create | sequence_db.read() read | sequence_db.filter() cluster | TOP to Python correspondence
sequence_db.read()
  Changes since release 8v2 | sequence_db() create | sequence_db.read() read | sequence_db.convert() convert | sequence_db.search() search | sequence_db.filter() cluster | Profile file | TOP to Python correspondence
sequence_db.search()
  The `sequence_db` class: using | sequence_db.search() search | TOP to Python correspondence
sequence_db.write()
  Changes since release 8v2 | sequence_db.write() write | sequence_db.convert() convert | TOP to Python correspondence
sge_pe_job
  sge_pe_job() create
sge_pe_job()
  sge_pe_job() create
sge_pe_slave
  sge_pe_slave() create
sge_pe_slave()
  sge_pe_slave() create
sge_qsub_job
  sge_qsub_job() create
sge_qsub_job()
  Changes since release 9v1 | sge_qsub_job() create | job.run_all_tasks() run
sge_qsub_slave
  sge_qsub_slave() create
sge_qsub_slave()
  sge_qsub_slave() create
sheet
  sheet() make
sheet()
  sheet() make
sheet_h_bonds
  sheet() make
signif_cutoff
  sequence_db.search() search
similarity_flag
  Features of proteins used | Alignments using external restraints | Useful SALIGN information and
skip
  actions.write_structure() write | actions.trace() write | actions.charmm_trajectory() write
slave.run_cmd()
  Parallel job support | job() create | communicator.send_data() send | slave.run_cmd() run
smoothing_window
  selection.energy() evaluate
soft-sphere
  Frequently asked questions (FAQ) | `dope_loopmodel` reference | Static and dynamic restraints | The `energy_data` class: objective | energy_data.update_dynamic nonbond | energy_data.sphere_stdv soft-sphere | energy_data.dynamic_sphere calculate | energy_data.radii_factor scale | restraints.make() make | physical.values() create | schedule() create | Function
spaceflag
  saxsdata.ini_saxs() Initialization
special_patches
  automodel.special_patches() add | model.build_sequence() build | complete_pdb() read
special_restraints
  automodel.special_restraints() add
spline
  restraints.spline() approximate
spline_dx
  restraints.make() make | restraints.spline() approximate
spline_min_points
  restraints.make() make | restraints.spline() approximate
spline_on_site
  restraints.make() make
spline_range
  restraints.make() make
ssh_command
  ssh_slave() create
ssh_slave
  ssh_slave() create
ssh_slave()
  ssh_slave() create
start
  model.atom_range() return | model.residue_range() return | actions.write_structure() write | job.start() start
start_type
  density.grid_search() dock
state_optimizer()
  Changes since release 8v2
statistical potential
  Loop modeling method
stdev
  Mathematical forms of restraints
stdevs
  Mathematical forms of restraints
steps
  schedule() create
strand
  strand() make
strand()
  strand() make | sheet() make
structure_types
  model.make_chains() Fetch
submodel
  topology.make() make
subopt_offset
  Sub-optimal alignments
summary_file
  Changes since release 9v1 | profile.scan() Compare
superpose
  selection.superpose() superpose
superpose_data
  selection.superpose() superpose
superpose_refine
  selection.superpose() superpose
surftyp
  model.write_data() write
swap_atoms_in_res
  selection.superpose() superpose
symmetry
  Symmetry restraints
symmetry restraints
  Symmetry restraints
system
  environ.system() execute
temperature
  molecular_dynamics() optimize | density.grid_search() dock
terms
  selection.energy() evaluate
time_mark
  info.time_mark() print
to_alignment
  profile.to_alignment() profile
to_iupac
  model.to_iupac() standardize
to_profile
  alignment.to_profile() convert
topology.append()
  libraries.topology topology | topology.append() append | topology.read() read | selection.rotate_dihedrals() change | TOP to Python correspondence
topology.clear()
  topology.append() append | topology.clear() clear | topology.read() read
topology.make()
  topology.append() append | topology.make() make | topology.submodel select | topology.write() write | TOP to Python correspondence
topology.read()
  automodel() prepare | topology.read() read | topology.submodel select | TOP to Python correspondence
topology.submodel
  Frequently asked questions (FAQ) | Changes since release 8v0 | energy_data.radii_factor scale | topology.append() append | topology.make() make | topology.submodel select | model.generate_topology() generate | model.patch_ss() guess | model.write_data() write | TOP to Python correspondence
topology.write()
  topology.write() write | TOP to Python correspondence
trace
  actions.trace() write
trace_output
  Changes since release 8v2
transfer_res_num
  complete_pdb() read
transfer_res_prop
  alnsequence.transfer_res_prop() transfer
transfer_xyz
  model.transfer_xyz() copy
transform
  selection.transform() transform
translate
  selection.translate() translate
translate_type
  density.grid_search() dock
tutorial
  Using MODELLER for comparative
unbuild
  selection.unbuild() undefine
unpick
  restraints.unpick() unselect
unpick_all
  restraints.unpick_all() unselect
unpick_redundant
  restraints.unpick_redundant() unselected
use_conv
  saxsdata.ini_saxs() Initialization
use_lookup
  saxsdata.ini_saxs() Initialization
use_offset
  saxsdata.ini_saxs() Initialization
use_parallel_job
  automodel.use_parallel_job() parallelize
use_rolloff
  saxsdata.ini_saxs() Initialization
user_after_single_loop_model
  loopmodel.user_after_single_loop_model() analyze
user_after_single_model
  automodel.user_after_single_model() analyze
values
  Mathematical forms of restraints | physical.values() create
varatom
  Changes since release 9v1 | alignment.compare_structures() compare
variability_file
  alignment.compare_sequences() compare
variable target function method
  Changing the default optimization
verbose
  log.verbose() display
very_fast
  automodel.very_fast() request
very_verbose
  log.very_verbose() display
viol_report_cut
  selection.hot_atoms() atoms | selection.energy() evaluate
viol_report_cut2
  selection.energy() evaluate
virtual_atom.ch1
  Specification of pseudo atoms
virtual_atom.ch1a
  Specification of pseudo atoms
virtual_atom.ch2
  Specification of pseudo atoms
voxel_size
  density.read() read
VTFM
  see variable target function method
weights
  Mathematical forms of restraints
weights_type
  Features of proteins used
write
  topology.write() write | model.write() write | restraints.write() write | selection.write() write | schedule.write() write | alignment.write() write | profile.write() write | sequence_db.write() write
write_all_atoms
  actions.write_structure() write
write_data
  model.write_data() write
write_fit
  alignment.malign3d() align | Features of proteins used | Useful SALIGN information and
write_psf
  model.write_psf() write
write_structure
  actions.write_structure() write
write_whole_pdb
  alignment.malign3d() align | Useful SALIGN information and
wswitch
  saxsdata.ini_saxs() Initialization
z_comb
  model.assess_ga341() assess
z_pair
  model.assess_ga341() assess
z_surf
  model.assess_ga341() assess