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()

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_leading_gaps

Residue.add_leading_gaps() add

add_trailing_gaps

Residue.add_trailing_gaps() add

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.get_suboptimals() parse | alignment.segment_matching() align

align_code

Chain.write() write | Chain.atom_file_and_code() get

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 Structure class

The Structure class: a

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 | Gap penalties and correcting | sequence_db.filter() cluster | TOP to Python correspondence

alignment.align2d

Residue.curvature Mainchain

alignment.align2d()

Coordinate files and derivative | alignment.write() write | alignment.align2d() align | alignment.salign() align | Alignment of protein structures | TOP to Python correspondence

alignment.align3d()

selection.superpose() superpose | 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.read_one() 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 | Structure.reread() reread | Flowchart of comparative modeling | TOP to Python correspondence

alignment.check_sequence_structure()

alignment.check_sequence_structure() check | alignment.check() check

alignment.check_structure_structure()

alignment.check_structure_structure() check | alignment.check() check

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()

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.get_suboptimals()

Sub-optimal alignments | alignment.get_suboptimals() parse

alignment.id_table()

environ.dendrogram() clustering | environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_sequences() compare | Sequence.get_num_equiv() get | Sequence.get_sequence_identity() get | TOP to Python correspondence

alignment.malign()

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.compare_structures() compare | alignment.malign3d() align | alignment.salign() align | Features of proteins used | Structure.read() read | Flowchart of comparative modeling | TOP to Python correspondence

alignment.positions

alignment.positions list | Residue.get_aligned_residue() get

alignment.read_one()

alignment.read_one() read | modfile.File() open

alignment.salign

Residue.curvature Mainchain

alignment.salign()

alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used | Alignment of protein structures | Useful SALIGN information and | alignment.get_suboptimals() parse | Structure.read() read | The salign module: high-level | iterative_structural_align() obtain | TOP to Python correspondence

alignment.segment_matching()

alignment.segment_matching() align | TOP to Python correspondence

alignment.to_profile

environ.make_pssmdb() Create

alignment.to_profile()

alignment.to_profile() convert | profile() create | profile.to_alignment() profile | profile.scan() Compare | profile.build() Build | Profile file | TOP to Python correspondence

alignment.write()

selection.mutate() mutate | alignment.write() write | alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.malign3d() align | Chain.write() write | profile.build() Build | sequence_db.search() search | TOP to Python correspondence

alignment_features

alignment.write() write

alignment_format

alignment.write() write

alignment_type

Alignment of protein sequences | Alignment of protein structures

alignment_what

Alignment of protein sequences

allhmodel

allhmodel() prepare

allhmodel class

allhmodel reference

allhmodel()

allhmodel() prepare

allow_alternates

alignment.append() read

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 | alignment.compare_with() compare | sequence_db.search() search

aln_base_filename

profile.scan() Compare

alnfile

automodel() prepare | loopmodel() prepare

alnseq

model.generate_topology() generate

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

selection.assess() assess

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

assess_normalized_dope

model.assess_normalized_dope() assess

assessor

selection.assess() assess

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.accessibility

model.write_data() write | Atom.accessibility atomic

Atom.biso

model.write_data() write | model.make_region() define | Atom.biso isotropic

Atom.charge

Atom.charge electrostatic

Atom.dvx

Atom.dvx objective

Atom.get_equivalent_atom()

Restraints.make_distance() make | Atom.get_equivalent_atom() get

Atom.mass

Atom.mass mass

Atom.name

Atom.name PDB

Atom.occ

Atom.occ occupancy

Atom.residue

Atom.residue residue

Atom.type

automodel.special_patches() add | Block (BLK) residues with | Atom.type CHARMM

Atom.vx

Atom.vx x

atom1

sheet() make

atom2

sheet() make

atom_accessibility

model.make_region() define

atom_file

Structure.read() read | Chain.write() write | Chain.atom_file_and_code() get

atom_file_and_code

Chain.atom_file_and_code() get

atom_files

alignment.append() read | alignment.append_model() copy

atom_ids

Specification of pseudo atoms | Restraints.unpick() unselect

atom_range

model.atom_range() return

AtomScorer

soap_pp.AtomScorer() create

AtomType class

The AtomType class: a

AtomType.element

AtomType.element element

AtomType.mass

AtomType.mass atomic

AtomType.name

AtomType.name CHARMM

auto_align

automodel.auto_align() generate

auto_overhang

Alignment of protein structures

automodel

automodel() prepare

automodel class

automodel reference

automodel()

automodel() prepare | allhmodel() prepare | loopmodel() prepare

automodel.assess_methods

loopmodel() prepare | model.assess_ga341() assess | model.assess_normalized_dope() assess | selection.assess_dope() assess | selection.assess_dopehr() assess

automodel.auto_align()

Fully automated alignment and | automodel.auto_align() generate

automodel.cluster()

automodel.cluster() cluster

automodel.deviation

automodel.rand_method control | 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() prepare | automodel.final_malign3d final | loopmodel.loop.write_selection_only write | 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.guess_atom_type()

automodel.guess_atom_types() automatically | automodel.guess_atom_type() automatically

automodel.guess_atom_types()

automodel.special_patches() add | automodel.guess_atom_types() automatically | automodel.guess_atom_type() automatically | Block (BLK) residues with

automodel.initial_malign3d

Building a model from | automodel() prepare | automodel.initial_malign3d initial | model.transfer_xyz() copy | alignment.check_structure_structure() check

automodel.library_schedule

Changing the default optimization | automodel() prepare | automodel.library_schedule select | automodel.very_fast() request | 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_ca_ca_distance

automodel.max_ca_ca_distance Distance | automodel.max_n_o_distance Distance | automodel.max_sc_mc_distance Distance | automodel.max_sc_sc_distance Distance | automodel.very_fast() request

automodel.max_molpdf

Changing the default optimization | automodel.max_molpdf objective

automodel.max_n_o_distance

automodel.max_ca_ca_distance Distance | automodel.max_n_o_distance Distance

automodel.max_sc_mc_distance

automodel.max_ca_ca_distance Distance | automodel.max_sc_mc_distance Distance

automodel.max_sc_sc_distance

automodel.max_ca_ca_distance Distance | automodel.max_sc_sc_distance Distance

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 | automodel.very_fast() request | loopmodel.loop.md_level control

automodel.nonstd_restraints()

Including water molecules, HETATM | automodel.nonstd_restraints() add | Block (BLK) residues with | Flowchart of comparative modeling

automodel.outputs

Accessing output data after | automodel.outputs all | loopmodel.loop.outputs all

automodel.rand_method

automodel() prepare | automodel.rand_method control | automodel.very_fast() request

automodel.repeat_optimization

Changing the default optimization | automodel.repeat_optimization number

automodel.select_atoms()

Refining only part of | automodel.select_atoms() select

automodel.set_output_model_format()

Generating new-style PDBx/mmCIF outputs | Changes since release 9.13 | automodel.set_output_model_format() set | automodel.get_model_filename() get

automodel.special_patches()

Including disulfide bridges | Residues and chains in | automodel.special_patches() add | automodel.guess_atom_types() automatically | Flowchart of comparative modeling

automodel.special_restraints()

Adding additional restraints to | Building multi-chain models | 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 | automodel.user_after_single_model() analyze | loopmodel.user_after_single_loop_model() analyze

automodel.very_fast()

Getting a very fast | automodel.max_ca_ca_distance Distance | 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

break_break_bonus

alignment.align() align | Gap penalties and correcting

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_chain

alignment.edit() edit

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

Chain class

The Chain class: a

Chain.atom_file_and_code()

Chain.write() write | Chain.atom_file_and_code() get

Chain.atoms

Chain.atoms all

Chain.filter()

model.make_chains() Fetch | Chain.filter() check | Chain.write() write | Chain.atom_file_and_code() get

Chain.join()

Chain.join() join

Chain.name

Chain.name chain

Chain.residues

Chain.residues all

Chain.write()

model.make_chains() Fetch | Chain.filter() check | Chain.write() write | Chain.atom_file_and_code() get

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

check_sequence_structure

alignment.check_sequence_structure() check

check_structure_structure

alignment.check_structure_structure() check

chop_nonstd_termini

Chain.filter() check | Chain.write() write

cispeptide

cispeptide() creates

cispeptide()

Restraints.add() add | Restraints.unpick() unselect | cispeptide() creates

classes

group_restraints() create | group_restraints.append() read

clean_sequences

sequence_db.read() read

clear

Topology.clear() clear | Parameters.clear() clear | Restraints.clear() delete | alignment.clear() delete

clear_topology

model.clear_topology() clear

close

sequence_db.close() close

cluster

automodel.cluster() cluster

cluster_cut

automodel.cluster() cluster | model.transfer_xyz() copy

cluster_method

model.transfer_xyz() copy

color

model.color() color

comment

Chain.write() write

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

comparison_type

Alignment of protein sequences

complete_pdb

model.write_psf() write | complete_pdb() read

complete_pdb()

model.read() read | model.build_sequence() build | model.write() write | selection.assess_dope() assess | Chain.join() join | complete_pdb() read

compressed files

Reading or writing files

condense

Restraints.condense() remove

conjugate_gradients

conjugate_gradients() optimize

conjugate_gradients()

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 | Rigid bodies | 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 | physical.values() create | Function | Coulomb restraint

csrfile

automodel() prepare

current_directory

alignment.malign3d() align | Useful SALIGN information and

cutoff

gbsa.Scorer() create

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

density.grid Density

density.grid_search()

The density class: handling | density() create | density.read() read | density.grid_search() dock | TOP to Python correspondence

density.px

density.px Origin

density.py

density.py Origin

density.pz

density.pz Origin

density.read()

Changes since release 9.13 | density() create | density.resolution Map | density.voxel_size Map | density.px Origin | density.py Origin | density.pz Origin | density.read() read | density.grid_search() dock | TOP to Python correspondence

density.resolution

density.resolution Map | density.sigma_factor Sigma

density.sigma_factor

density.sigma_factor Sigma

density.voxel_size

density.voxel_size Map

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()

dope_loopmodel() prepare | The gbsa module: implicit

dopehr_loopmodel class

dopehr_loopmodel reference

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 | energy_data.nlogn_use select | Restraints.make() make | selection.assess_dope() assess | conjugate_gradients() optimize | gbsa.Scorer() create | soap_loop.Scorer() create | Atomic density | TOP to Python correspondence

energy_data.coulomb_switch

energy_data.contact_shell nonbond | energy_data.coulomb_switch Coulomb | gbsa.Scorer() create | 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_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

Block (BLK) residues with | 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 | gbsa.Scorer() create | soap_loop.Scorer() create | 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 | selection.assess_dope() assess | 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.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

EnergyProfile class

The EnergyProfile class: a

EnergyProfile.get_normalized()

EnergyProfile.get_normalized() get

EnergyProfile.get_smoothed()

EnergyProfile.get_smoothed() get

EnergyProfile.heavy_rms

EnergyProfile.heavy_rms heavy

EnergyProfile.min_rms

EnergyProfile.min_rms minimal

EnergyProfile.write_to_file()

EnergyProfile.write_to_file() write

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

eqvdst

alignment.check_structure_structure() check

errors

EOFError

Controlling breakpoints and the

FileFormatError

Controlling breakpoints and the | model.read() read | alignment.append() read | alignment.read_one() read

handling and recovering

Controlling breakpoints and the

IndexError

Controlling breakpoints and the

IOError

Controlling breakpoints and the

MemoryError

Controlling breakpoints and the

ModellerError

Controlling breakpoints and the | model.assess_ga341() assess

NetworkError

Communicator.send_data() send

NotImplementedError

Controlling breakpoints and the | Restraints.spline() approximate

RemoteError

Communicator.send_data() send

SequenceMismatchError

alignment.append() read | alignment.read_one() read

standard Python

Controlling breakpoints and the

StatisticsError

profile.build() Build

TypeError

Controlling breakpoints and the

UnicodeError

Controlling breakpoints and the | Unicode

ValueError

Controlling breakpoints and the | Restraints.spline() approximate | alignment.append_model() copy | Chain.join() join

ZeroDivisionError

Controlling breakpoints and the

exclude_distance

Restraints.make_distance() make

excluded pairs

Excluded pairs

excluded_pair

Excluded pairs

exit_stage

automodel.make() build

ext_tree_file

Alignments using external restraints

extend_by_residue

selection.extend_by_residue() extend

extension

model.get_insertions() return | model.get_deletions() return | selection.extend_by_residue() extend

extra_data

model.write() write

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

Alignment of protein sequences | 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 | Topology.write() write | model.read() read | model.write() write | model.write_data() write | Restraints.append() read | Restraints.write() write | group_restraints.append() read | alignment.append() read | alignment.read_one() read | alignment.write() write | alignment.segment_matching() align | Structure.write() write | Structure.read() read | Chain.write() write | profile.read() read | profile.write() write | density.read() read | modfile.File() open

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

Chain.filter() check | sequence_db.filter() cluster

filter_type

density.read() read

filter_values

density.read() read

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

format

Chain.write() write

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 structures | Sub-optimal alignments | Residue.curvature Mainchain

gap_gap_score

Gap penalties and correcting

gap_penalties_1d

alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.salign() align | Gap penalties and correcting | profile.scan() Compare | sequence_db.search() search | sequence_db.filter() cluster | Profile file

gap_penalties_2d

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

gapdist

alignment.check_sequence_structure() check

gaps_in_target

profile.build() Build

GB/SA scoring

gbsa.Scorer() create

gbsa.Scorer()

Block (BLK) residues with | gbsa.Scorer() create

generate_topology

model.generate_topology() generate

get_aligned_residue

Residue.get_aligned_residue() get

get_data

Communicator.get_data() get

get_deletions

model.get_deletions() return

get_dope_profile

selection.get_dope_profile() get

get_dopehr_profile

selection.get_dopehr_profile() get

get_equivalent_atom

Atom.get_equivalent_atom() get

get_insertions

model.get_insertions() return

get_leading_gaps

Residue.get_leading_gaps() get

get_loop_model_filename

loopmodel.get_loop_model_filename() get

get_model_filename

automodel.get_model_filename() get

get_normalized

EnergyProfile.get_normalized() get

get_normalized_dope_profile

model.get_normalized_dope_profile() get

get_num_equiv

Sequence.get_num_equiv() get

get_optimize_actions

automodel.get_optimize_actions() get

get_range

Restraints.spline() approximate

get_refine_actions

automodel.get_refine_actions() get

get_sequence_identity

Sequence.get_sequence_identity() get

get_smoothed

EnergyProfile.get_smoothed() get

get_suboptimals

alignment.get_suboptimals() parse

get_trailing_gaps

Residue.get_trailing_gaps() 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()

Block (BLK) residues with | 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

guess_atom_type

automodel.guess_atom_type() automatically

guess_atom_types

automodel.guess_atom_types() automatically

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

include_termini

model.get_insertions() return | model.get_deletions() return | model.loops() return

info.bindir

info.bindir MODELLER

info.build_date

info.version the | info.build_date the

info.debug

info.debug this

info.exe_type

info.exe_type the

info.jobname

info.jobname name | job() create

info.time_mark()

info.time_mark() print | TOP to Python correspondence

info.version

info.version the

info.version_info

info.version the | info.version_info the

ini_saxs

saxsdata.ini_saxs() Initialization

inifile

automodel() prepare

inimodel

loopmodel() prepare

init_velocities

molecular_dynamics() optimize

initialize_xyz

model.build() build

input_profile_file

alignment.align2d() align

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 | model.read() read

io_data.atom_files_directory

Simple usage | Coordinate files and derivative | io_data.atom_files_directory search | Alignment file (PIR) | TOP to Python correspondence

io_data.convert_modres

io_data() create | io_data.convert_modres whether

io_data.hetatm

Block (BLK) residues with | io_data() create | io_data.hetatm whether | io_data.convert_modres 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.hetatm whether | io_data.water whether | TOP to Python correspondence

iterative_structural_align

iterative_structural_align() obtain

iterative_structural_align()

Alignment of protein structures | iterative_structural_align() obtain

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.yield_tasks_unordered() run

job.slave_startup_commands

job() create | job.slave_startup_commands Slave

job.start()

Parallel job support | job() create | job.start() start

job.yield_tasks_unordered()

Parallel job support | job() create | job.queue_task() submit | job.run_all_tasks() run | job.yield_tasks_unordered() run

join

Chain.join() join

knowns

Building a model from | automodel() prepare | loopmodel() prepare | alignment.check_structure_structure() check

last

actions.write_structure() write | actions.charmm_trajectory() write

last_scales

schedule() create | schedule.make_for_model() trim

Lennard-Jones

Frequently asked questions (FAQ) | automodel.guess_atom_types() automatically | dope_loopmodel reference | Residues with defined topology, | Block (BLK) residues with | Static and dynamic restraints | Mathematical forms of restraints | Rigid bodies | energy_data.contact_shell nonbond | energy_data.dynamic_lennard calculate | energy_data.lennard_jones_switch Lennard-Jones | Restraints.make() make | 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

gbsa.Scorer() create | soap_loop.Scorer() create

library_schedule

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()

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 | model.assess_ga341() assess | model.assess_normalized_dope() assess | selection.assess_dope() assess | selection.assess_dopehr() assess

loopmodel.loop.ending_model

Automatic loop refinement after | loopmodel.loop.ending_model last | Loop modeling method

loopmodel.loop.library_schedule

loopmodel.loop.library_schedule select

loopmodel.loop.max_var_iterations

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.loop.write_defined_only

loopmodel.loop.write_defined_only only

loopmodel.loop.write_selection_only

loopmodel.loop.write_selection_only write | loopmodel.loop.write_defined_only only

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()

automodel.user_after_single_model() analyze | 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

make_valid_pdb_coordinates

model.make_valid_pdb_coordinates() make

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

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_gap_length

alignment.align2d() align

max_gaps_match

alignment.compare_sequences() compare

max_iterations

automodel.max_var_iterations select | conjugate_gradients() optimize | molecular_dynamics() optimize

max_nonstdres

Chain.filter() check

max_unaligned_res

sequence_db.filter() cluster

max_var_iterations

automodel.very_fast() request

maximal_distance

automodel.max_ca_ca_distance 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 | schedule.make_for_model() trim | alignment.append_model() copy | alignment.compare_sequences() compare | complete_pdb() read

mdl2

selection.superpose() superpose

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

Chain.filter() check

minimal_resolution

Chain.filter() check

minimal_stdres

Chain.filter() check

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

mmCIF 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.transfer_xyz() copy | 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

mode

modfile.File() open

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.assess_normalized_dope()

automodel() prepare | model.assess_normalized_dope() assess | model.get_normalized_dope_profile() get | selection.assess_dope() assess

model.atom_range()

Feature types | model.atoms all | model.atom_range() return | The selection class: handling

model.atoms

Residues and chains in | 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 | selection.only_defined() select | Flowchart of comparative modeling | TOP to Python correspondence

model.build_sequence()

model.build_sequence() build | alignment.append_sequence() add

model.clear_topology()

model.clear_topology() clear | model.generate_topology() generate

model.color()

model.color() color | TOP to Python correspondence

model.generate_topology()

Frequently asked questions (FAQ) | energy_data.dynamic_sphere calculate | energy_data.dynamic_lennard calculate | 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.get_normalized_dope_profile()

model.get_normalized_dope_profile() get | The EnergyProfile class: a

model.group_restraints

energy_data.dynamic_modeller calculate | model.group_restraints all

model.last_energy

model.last_energy last | model.write() write

model.loops()

loopmodel.select_loop_atoms() select | model.get_insertions() return | model.get_deletions() return | model.loops() return | The selection class: handling

model.make_chains()

model.make_chains() Fetch | Chain.filter() check | TOP to Python correspondence

model.make_region()

model.make_region() define | Atom.biso isotropic | TOP to Python correspondence

model.make_valid_pdb_coordinates()

model.make_valid_pdb_coordinates() make

model.orient()

model.orient() center | TOP to Python correspondence

model.patch()

Including disulfide bridges | Frequently asked questions (FAQ) | automodel.special_patches() add | 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 9.13 | Residues with defined topology, | model() create | model.remark text | 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 | Sequence.range residue | Sequence.rfactor R | complete_pdb() read | Flowchart of comparative modeling | TOP to Python correspondence

model.remark

model.remark text | model.write() write

model.rename_segments()

Residues and chains in | 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.residue_range() return | alpha() make | strand() make | The selection class: handling | Sequence.residues list

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.write() write | model.assess_ga341() assess

model.to_iupac()

Changes since release 9.13 | 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 | selection.only_defined() select | alignment.malign3d() align | Flowchart of comparative modeling | TOP to Python correspondence

model.write()

Changes since release 9.13 | model.seq_id sequence | model.last_energy last | model.read() read | model.write() write | model.write_data() write | model.make_region() define | model.color() color | selection.write() write | Chain.join() join | modfile.File() open | Flowchart of comparative modeling | TOP to Python correspondence

model.write_data

Residue.curvature Mainchain

model.write_data()

Feature types | energy_data.radii_factor scale | model.write() write | model.write_data() write | model.make_region() define | Atom.biso isotropic | Atom.accessibility atomic | Atomic solvent accessibility | TOP to Python correspondence

model.write_psf()

model.write_psf() write | actions.charmm_trajectory() write

model_segment

model.read() read | Sequence.range residue | 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.File()

automodel() prepare | Reading or writing files | environ() create | Topology.append() append | Parameters.append() append | Topology.write() write | model.read() read | model.write() write | model.write_psf() write | Restraints.append() read | Restraints.write() write | schedule.write() write | group_restraints() create | group_restraints.append() read | alignment.append() read | alignment.read_one() read | alignment.write() write | alignment.id_table() calculate | Structure.write() write | Structure.read() read | Chain.write() write | EnergyProfile.write_to_file() write | profile.read() read | profile.write() write | density.read() read | modfile.File() open

modfile.inquire()

modfile.inquire() check | TOP to Python correspondence

molecular_dynamics

molecular_dynamics() optimize

molecular_dynamics()

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_exceed

selection.debug_function() test

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

ngap

Residue.add_leading_gaps() add | Residue.add_trailing_gaps() add | Residue.remove_leading_gaps() remove | Residue.remove_trailing_gaps() remove

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

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_defined

selection.only_defined() 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

only_water_residues

selection.only_water_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

OrientData

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

PairScorer

soap_pp.PairScorer() create

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.transfer_xyz() copy | 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 | strand() make | sheet() make | 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()

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()

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()

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

protonation states

model.read() read

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

pssm_file

profile.build() Build

pssmdb

pssmdb() create

pssmdb()

pssmdb() create

pssmdb.read()

pssmdb() create | pssmdb.read() read

pssmdb_name

environ.make_pssmdb() Create

px

density.read() read

py

density.read() read

Python

installation

Obtaining and installing the

license

Copyright notice

used by MODELLER

Script file

using MODELLER as a Python module

Running MODELLER

pz

density.read() read

q1

Mathematical forms of restraints

q2

Mathematical forms of restraints

quasi_newton

quasi_newton() optimize

quasi_newton()

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 | Structure.read() read | profile.read() read | pssmdb.read() read | sequence_db.read() read | density.read() read

read_one

alignment.read_one() read

read_potential

loopmodel.read_potential() read

reference_atom

selection.superpose() superpose

reference_distance

selection.superpose() superpose

refine_local

selection.superpose() superpose

region_size

model.make_region() define

reindex

Restraints.reindex() renumber

remove_gaps

alignment.append() read | alignment.read_one() read

remove_leading_gaps

Residue.remove_leading_gaps() remove

remove_trailing_gaps

Residue.remove_trailing_gaps() remove

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

reread

Structure.reread() reread

res_num_from

model.res_num_from() residue

Residue class

The Residue class: a

Residue.add_leading_gaps()

Residue.add_leading_gaps() add

Residue.add_trailing_gaps()

Residue.add_trailing_gaps() add

Residue.alpha

Residue.alpha $\alpha$

Residue.atoms

Residue.atoms all

Residue.chain

Residue.chain chain

Residue.chi1

Residue.chi1 $\chi _1$

Residue.chi2

Residue.chi2 $\chi _2$

Residue.chi3

Residue.chi3 $\chi _3$

Residue.chi4

Residue.chi4 $\chi _4$

Residue.chi5

Residue.chi5 $\chi _5$

Residue.code

Residue.code One-letter

Residue.curvature

Residue.curvature Mainchain

Residue.get_aligned_residue()

Residue.get_aligned_residue() get

Residue.get_leading_gaps()

Residue.get_leading_gaps() get

Residue.get_trailing_gaps()

Residue.get_trailing_gaps() get

Residue.hetatm

Residue.hetatm HETATM

Residue.index

Residue.index internal | Residue.num PDB-style

Residue.name

Residue.name internal

Residue.num

Residue.num PDB-style

Residue.omega

Residue.omega $\omega$

Residue.pdb_name

Residue.pdb_name PDB

Residue.phi

Residue.phi $\phi$ | Residue.psi $\psi$ | Residue.omega $\omega$ | Residue.alpha $\alpha$ | Residue.chi1 $\chi _1$ | Residue.chi2 $\chi _2$ | Residue.chi3 $\chi _3$ | Residue.chi4 $\chi _4$ | Residue.chi5 $\chi _5$ | The Dihedral class: a

Residue.psi

Residue.psi $\psi$

Residue.remove_leading_gaps()

Residue.remove_leading_gaps() remove

Residue.remove_trailing_gaps()

Residue.remove_trailing_gaps() remove

residue_range

model.residue_range() return

residue_span_range

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

Restraints.make() make | Restraints.unpick_redundant() unselect

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() unselect | Restraints.remove_unpicked() remove | Restraints.condense() remove | Restraints.unpick() unselect | Restraints.reindex() renumber | alpha() make | strand() make | TOP to Python correspondence

Restraints.excluded_pairs

Excluded pairs | Restraints.excluded_pairs all

Restraints.make()

Frequently asked questions (FAQ) | Coordinate files and derivative | Residues with defined topology, | 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 | Atomic solvent accessibility | Flowchart of comparative modeling | TOP to Python correspondence

Restraints.make_distance()

Frequently asked questions (FAQ) | automodel.max_ca_ca_distance Distance | Block (BLK) residues with | Restraints.make() make | Restraints.make_distance() make | Atom.get_equivalent_atom() get | Atomic solvent accessibility

Restraints.nonbonded_pairs

Restraints.nonbonded_pairs all

Restraints.pick()

Frequently asked questions (FAQ) | 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()

Restraints.make() make | Restraints.spline() approximate | User-defined restraint forms | TOP to Python correspondence

Restraints.symmetry

Symmetry restraints | Restraints.symmetry all

Restraints.symmetry.report()

Restraints.symmetry.report() report

Restraints.unpick()

Frequently asked questions (FAQ) | Restraints.unpick() unselect | alpha() make | strand() make | TOP to Python correspondence

Restraints.unpick_all()

Restraints.unpick_all() unselect | Restraints.pick() pick

Restraints.unpick_redundant()

Restraints.make() make | Restraints.unpick_redundant() unselect | Restraints.condense() remove

Restraints.write()

Static and dynamic restraints | Restraints.write() write | Flowchart of comparative modeling | TOP to Python correspondence

restraints_filter

Restraints.pick() pick

restyp_lib_file

environ() create

rho_solv

saxsdata.ini_saxs() Initialization

rigid bodies

Rigid bodies

rigid_body

Rigid bodies

rms_cutoff

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

SalignData

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()

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 | selection.assess() assess | conjugate_gradients() optimize

score

model.assess_ga341() assess | selection.assess() assess

score_statistics

profile.scan() Compare

Scorer

gbsa.Scorer() create | soap_loop.Scorer() create | soap_peptide.Scorer() create | soap_protein_od.Scorer() create

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()

selection.assess_dope() assess | selection.assess() assess | soap_loop.Scorer() create | soap_protein_od.Scorer() create

selection.assess_dope()

automodel() prepare | dope_loopmodel reference | Rigid bodies | model.assess_normalized_dope() assess | selection.assess_dope() assess | selection.assess_dopehr() assess | selection.get_dope_profile() get | selection.assess() assess | Sequence.chains list

selection.assess_dopehr()

automodel() prepare | dopehr_loopmodel reference | selection.assess_dopehr() assess | selection.get_dopehr_profile() get

selection.by_residue()

The selection class: handling | selection.by_residue() make

selection.debug_function()

selection.debug_function() test | physical.values() create | TOP to Python correspondence

selection.energy()

Including disulfide bridges | Frequently asked questions (FAQ) | Changes since release 9.13 | Mathematical forms of restraints | model.write() write | model.generate_topology() generate | Restraints.nonbonded_pairs all | selection.energy() evaluate | selection.debug_function() test | selection.assess_dope() assess | selection.assess() assess | Atom.biso isotropic | EnergyProfile.get_smoothed() get | complete_pdb() read | Function | Flowchart of comparative modeling | TOP to Python correspondence

selection.extend_by_residue()

selection.extend_by_residue() extend | selection.hot_atoms() atoms

selection.get_dope_profile()

selection.get_dope_profile() get | The EnergyProfile class: a

selection.get_dopehr_profile()

selection.get_dopehr_profile() get | The EnergyProfile class: a

selection.hot_atoms()

model.generate_topology() generate | selection.hot_atoms() atoms | Function | TOP to Python correspondence

selection.mutate()

selection.mutate() mutate | TOP to Python correspondence

selection.only_atom_types()

The selection class: handling | selection.only_atom_types() select

selection.only_defined()

The selection class: handling | selection.only_defined() 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.only_water_residues()

The selection class: handling | selection.only_water_residues() select

selection.randomize_xyz()

selection.randomize_xyz() randomize | schedule() create | Flowchart of comparative modeling | TOP to Python correspondence

selection.rotate_dihedrals()

selection.rotate_dihedrals() change | TOP to Python correspondence

selection.rotate_mass_center()

selection.rotate_origin() rotate | selection.rotate_mass_center() rotate

selection.rotate_origin()

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()

selection.superpose() superpose | alignment.compare_structures() compare | TOP to Python correspondence

selection.transform()

selection.rotate_origin() rotate | selection.rotate_mass_center() rotate | selection.transform() transform | TOP to Python correspondence

selection.translate()

selection.translate() translate | TOP to Python correspondence

selection.unbuild()

selection.unbuild() undefine | TOP to Python correspondence

selection.write()

model.write() write | selection.write() write

selection_segment

Alignment file (PIR)

send_data

Communicator.send_data() send

seq

Sequence.get_num_equiv() get | Sequence.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 class

The Sequence class: a

Sequence.atom_file

model.generate_topology() generate | alignment.append_model() copy | alignment.malign3d() align | Sequence.atom_file PDB | Structure.reread() reread | Structure.read() read | TOP to Python correspondence

Sequence.chains

The model class: handling | model.atoms all | The selection class: handling | Sequence.chains list | The Chain class: a

Sequence.code

alignment.append_model() copy | Sequence.code alignment | Alignment file (PIR) | Profile file | TOP to Python correspondence

Sequence.get_num_equiv()

Sequence.get_num_equiv() get

Sequence.get_sequence_identity()

Sequence.get_sequence_identity() get

Sequence.name

Sequence.name protein

Sequence.prottyp

Sequence.prottyp protein

Sequence.range

Sequence.range residue

Sequence.residues

Residues and chains in | Feature types | The model class: handling | model.atoms all | model.residue_range() return | The selection class: handling | Sequence.residues list | The Residue class: a

Sequence.resolution

Sequence.resolution structure

Sequence.rfactor

model.read() read | Sequence.rfactor R

Sequence.source

Sequence.source source

Sequence.transfer_res_prop()

alignment.write() write | Sequence.transfer_res_prop() transfer

sequence_db

sequence_db() create

sequence_db class

The sequence_db class: using

sequence_db()

sequence_db() create

sequence_db.close()

sequence_db.close() close

sequence_db.convert()

sequence_db.read() read | sequence_db.convert() convert

sequence_db.filter()

The sequence_db class: using | sequence_db() create | sequence_db.read() read | sequence_db.filter() cluster | TOP to Python correspondence

sequence_db.read()

alignment.append() read | profile.build() Build | sequence_db() create | sequence_db.read() read | sequence_db.write() write | 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()

sequence_db.write() write | sequence_db.convert() convert | TOP to Python correspondence

set_output_model_format

automodel.set_output_model_format() set

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()

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 | Alignment of protein sequences | Sub-optimal alignments | 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

soap_loop.Scorer()

automodel() prepare | selection.assess() assess | soap_loop.Scorer() create | soap_peptide.Scorer() create | soap_protein_od.Scorer() create

soap_peptide.Scorer()

soap_peptide.Scorer() create

soap_pp.AtomScorer()

soap_pp.AtomScorer() create

soap_pp.PairScorer()

soap_pp.PairScorer() create | soap_pp.AtomScorer() create

soap_protein_od.Scorer()

automodel() prepare | selection.assess() assess | soap_protein_od.Scorer() create

soft-sphere

Frequently asked questions (FAQ) | automodel.guess_atom_types() automatically | dope_loopmodel reference | Block (BLK) residues with | 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

solvation_model

gbsa.Scorer() create

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

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.read()

Structure.read() read

Structure.reread()

Structure.reread() reread | Structure.read() read

Structure.write()

Structure.write() write

structure_types

Chain.filter() check

submodel

Topology.make() make

subopt_offset

Sub-optimal alignments

summary_file

profile.scan() Compare

superpose

selection.superpose() superpose

superpose_refine

selection.superpose() superpose

SuperposeData

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) | 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

transfer_res_num

complete_pdb() read

transfer_res_prop

Sequence.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

Unicode

Unicode

unpick

Restraints.unpick() unselect

unpick_all

Restraints.unpick_all() unselect

unpick_redundant

Restraints.unpick_redundant() unselect

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

UTF-8

Unicode

values

Mathematical forms of restraints | physical.values() create

varatom

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

window

EnergyProfile.get_smoothed() get

window_size

profile.build() Build | sequence_db.read() read | sequence_db.write() write | sequence_db.search() search | sequence_db.filter() cluster

write

Topology.write() write | model.write() write | Restraints.write() write | selection.write() write | schedule.write() write | alignment.write() write | Structure.write() write | Chain.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_to_file

EnergyProfile.write_to_file() write

write_whole_pdb

alignment.malign3d() align | Useful SALIGN information and

wswitch

saxsdata.ini_saxs() Initialization

yield_tasks_unordered

job.yield_tasks_unordered() run

Z-score

model.assess_normalized_dope() assess

z_comb

model.assess_ga341() assess

z_pair

model.assess_ga341() assess

z_surf

model.assess_ga341() assess