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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()
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.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 | TOP to Python correspondence
alignment.align2d()
Changes since release 9v4 | 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()
Changes since release 9v3 | 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()
Changes since release 9v4 | Changes since release 9v3 | 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) | Changes since release 9v3 | alignment.check() check | Structure.reread() reread | Flowchart of comparative modeling | TOP to Python correspondence
alignment.check_sequence_structure()
Changes since release 9v3 | alignment.check_sequence_structure() check | alignment.check() check
alignment.check_structure_structure()
Changes since release 9v3 | 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()
Changes since release 9v3 | 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.read_one()
Changes since release 9v3 | alignment.read_one() read | modfile.File() open
alignment.salign()
Changes since release 9v3 | 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 | 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.build() Build | Profile file | TOP to Python correspondence
alignment.write()
Changes since release 9v3 | 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
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 | 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_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
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.element
Atom.element Element
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_file
Chain.write() write | Chain.atom_file_and_code() get
atom_file_and_code
Chain.atom_file_and_code() get
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()
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 | 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 | 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 | 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 | 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.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
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.name
Chain.name chain
Chain.residues
Chain.residues all
Chain.write()
Changes since release 9v3 | 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_file
Changes since release 9v3
cluster
automodel.cluster() cluster
cluster_cut
Changes since release 9v3 | 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
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 | 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_search()
Changes since release 9v3 | 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_atoms
Changes since release 9v4
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 | Restraints.make() make | conjugate_gradients() optimize | gbsa.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
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 | 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.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
eqvdst
alignment.check_structure_structure() check
errors
FileFormatError
Controlling breakpoints and the | model.read() read | alignment.append() read | alignment.read_one() read
handling and recovering
Controlling breakpoints and the
ModellerError
Controlling breakpoints and the | model.assess_ga341() assess
standard Python
Controlling breakpoints and the
exclude_distance
Restraints.make_distance() make
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
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() write | model.write_data() write | group_restraints.append() read | alignment.read_one() read | alignment.write() write | alignment.segment_matching() align | Structure.write() write | Chain.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 sequences | Alignment of protein structures
gap_gap_score
Gap penalties and correcting
gap_penalties_1d
Changes since release 9v4 | 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()
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_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_num_equiv
Sequence.get_num_equiv() get
get_optimize_actions
automodel.get_optimize_actions() get
get_refine_actions
automodel.get_refine_actions() get
get_sequence_identity
Sequence.get_sequence_identity() get
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()
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 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
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
io_data.atom_files_directory
Simple usage | Changes since release 9v3 | 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 | 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) | 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
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
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.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()
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
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
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 | 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
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()
Changes since release 9v4 | automodel() prepare | model.assess_normalized_dope() 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 | 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.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 | Chain.filter() check | 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) | 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()
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 | Sequence.range residue | 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.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.assess_ga341() assess
model.to_iupac()
model() create | model.to_iupac() standardize | TOP to Python correspondence
model.transfer_xyz()
Changes since release 9v3 | 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 9v3 | 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 | 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()
Changes since release 9v3 | model.write() write | alignment.read_one() read | alignment.write() write | Structure.write() write | Chain.write() write | 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
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 | 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
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()
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_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.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.name
Residue.name internal
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_grouping
Changes since release 9v4
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) | Changes since release 9v4 | 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) | Block (BLK) residues with | Restraints.make() make | Restraints.make_distance() make | Atomic solvent accessibility
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 | 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
rewind_file
Changes since release 9v3
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 | conjugate_gradients() optimize
score
model.assess_ga341() assess
score_statistics
profile.scan() Compare
Scorer
gbsa.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_dope()
automodel() prepare | dope_loopmodel reference | Rigid bodies | model.assess_normalized_dope() assess | selection.assess_dope() assess | selection.assess_dopehr() assess | Sequence.chains list
selection.assess_dopehr()
automodel() prepare | dopehr_loopmodel reference | selection.assess_dopehr() assess
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) | 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()
selection.extend_by_residue() extend | selection.hot_atoms() atoms
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()
Changes since release 9v4 | 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()
Changes since release 9v3 | 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()
Changes since release 9v3 | 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 | Alignment file (PIR) | 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
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
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.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()
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()
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()
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
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.reread()
Structure.reread() reread
Structure.write()
Changes since release 9v3 | 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()
Changes since release 9v4 | 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
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
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
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_whole_pdb
alignment.malign3d() align | Useful SALIGN information and
wswitch
saxsdata.ini_saxs() Initialization
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


Automatic builds 2008-10-07