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Index

accessibility_type
model.write_data() write | model.restraints.make() make
add_segment
model.generate_topology() generate
add_symmetry
model.symmetry.define() define
align3d_repeat
alignment.align3d() align
align3d_trf
alignment.align3d() align | alignment.salign() align | Features of proteins used
align_alignment
alignment.write() write
align_block
alignment.write() write | alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.consensus() consensus | alignment.salign() align | Alignment of protein sequences | alignment.segment_matching() align
align_codes
alignment.append() read | alignment.append_model() copy
align_what
alignment.align() align | alignment.align2d() align | alignment.salign() align | Alignment of protein sequences
alignment
Alignment file | Alignment file format
alignment()
alignment() create
alignment.align
Alignment of protein structures
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
Alignment of protein structures
alignment.align2d()
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()
model.superpose() superpose | alignment.align() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used | TOP to Python correspondence
alignment.append()
alignment() create | alignment.append() read | alignment.compare_with() compare | alignment.write() write | alignment.describe() describe | profile.build() Build | TOP to Python correspondence | Flowchart of comparative modeling
alignment.append_model()
model.mutate() mutate | alignment.append_model() copy | TOP to Python correspondence
alignment.append_profile()
alignment() create | alignment.append_profile() add | TOP to Python correspondence
alignment.check()
Alignment file | Running MODELLER | Frequently asked questions (FAQ) | Fully automated alignment and | alignment.check() check | TOP to Python correspondence | Flowchart of comparative modeling
alignment.clear()
alignment.clear() delete
alignment.compare_sequences()
environ.dendrogram() clustering | environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_sequences() compare | TOP to Python correspondence
alignment.compare_structures()
Changes since release 7v7 | 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.append_model() copy | 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.expand()
alignment.expand() put | TOP to Python correspondence | Flowchart of comparative modeling
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 | TOP to Python correspondence | Flowchart of comparative modeling
alignment.salign
Alignment of protein structures
alignment.salign()
Changes since release 7v7 | alignment.salign() align | Features of proteins used | Useful SALIGN information and | TOP to Python correspondence
alignment.segment_matching()
alignment.segment_matching() align | TOP to Python correspondence
alignment.to_profile()
alignment.to_profile() convert | profile.read() read | profile.to_alignment() profile | profile.build() Build | TOP to Python correspondence
alignment.write()
model.mutate() mutate | alignment.write() write | alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.malign3d() align | profile.build() Build | sequence_db.search() search | TOP to Python correspondence
alignment[x].atom_file
model.generate_topology() generate | Alignment file format | alignment.append_model() copy | alignment.malign3d() align
alignment[x].code
Alignment file format | alignment.append_model() copy | profile.read() read
alignment_features
alignment.write() write | sequence_db.search() search
alignment_format
model.make_chains() Fetch | alignment.append() read | alignment.write() write
alignment_type
alignment.salign() align | Alignment of protein sequences | Alignment of protein structures
allhmodel()
allhmodel() prepare
aln
automodel.special_restraints() add | model.read() read | model.generate_topology() generate | model.patch_ss_templates() guess | model.transfer_xyz() copy | model.res_num_from() residue | model.pick_atoms() select | model.write_pdb_xref() write | model.color() color | model.superpose() superpose | model.restraints.make() make | alignment.compare_with() compare | sequence_db.search() search
aln_base_filename
profile.scan() Compare
alnfile
automodel() prepare | allhmodel() prepare | loopmodel() prepare
angular_step_size
density.grid_search() dock
asgl_output
model.energy() evaluate | alignment.compare_structures() compare
assess_methods
Getting a very fast | automodel() prepare | allhmodel() prepare | loopmodel() prepare
atom classes
Loop modeling method
atom_accessibility
model.make_region() define
atom_files
alignment.append() read | alignment.append_model() copy
atom_ids
model.restraints.make() make | model.restraints.add() add | model.restraints.unpick() unselect
atom_types
model.pick_atoms() select
auto_overhang
alignment.salign() align | Alignment of protein structures
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
automodel.starting_model first | automodel.ending_model last | loopmodel.loop.ending_model last | model.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.initial_malign3d
automodel.initial_malign3d initial
automodel.make()
Getting a very fast | Fully automated alignment and | automodel.outputs all | automodel.make() build
automodel.max_molpdf
automodel.max_molpdf objective
automodel.max_var_iterations
automodel.max_var_iterations select
automodel.md_level
automodel.md_level control | loopmodel.loop.md_level control
automodel.outputs
automodel.outputs all | loopmodel.loop.outputs all
automodel.rand_method
automodel.rand_method control
automodel.repeat_optimization
automodel.repeat_optimization number
automodel.select_atoms()
automodel.select_atoms() select
automodel.special_patches()
Frequently asked questions (FAQ) | automodel.special_patches() add | Flowchart of comparative modeling
automodel.special_restraints()
automodel.special_restraints() add | Flowchart of comparative modeling
automodel.starting_model
automodel.starting_model first | automodel.ending_model last | loopmodel.loop.starting_model first
automodel.user_after_single_model()
automodel.user_after_single_model() analyze
automodel.very_fast()
Getting a very fast | automodel.very_fast() request
automodel.write_intermediates
automodel.write_intermediates write
base_align_codes
alignment.edit() edit
basis_pdf_weight
model.restraints.make() make
basis_relative_weight
model.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_method
model.build() build
cap_atom_shift
model.optimize() optimize | Molecular dynamics
chains_list
sequence_db.read() read | sequence_db.write() write
change
model.rotate_dihedrals() change
check_profile
profile.build() Build
chop_nonstd_terminii
model.make_chains() Fetch
classes
group_restraints() create
clean_sequences
alignment.to_profile() convert | sequence_db.read() read
close_file
alignment.append() read
cluster_cut
automodel.cluster() cluster | environ.dendrogram() clustering | model.transfer_xyz() copy
cluster_method
model.transfer_xyz() copy
command
environ.system() execute
compare_mode
alignment.compare_structures() compare
comparison_type
alignment.salign() align
contact_shell
Formats of the restraints
csrfile
automodel() prepare | allhmodel() prepare | loopmodel() prepare
current_directory
alignment.malign3d() align | alignment.salign() align | Useful SALIGN information and
data_file
sequence_db.search() search
debug_function_cutoff
model.debug_function() test
dendrogram_file
alignment.salign() align | Alignment of protein structures | Useful SALIGN information and
density()
density() create
density.grid_search()
Changes since release 7v7 | 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_type
density.grid_search() dock
detailed_debugging
model.debug_function() test
deviation
automodel() prepare | allhmodel() prepare | loopmodel() prepare | model.randomize_xyz() randomize | model.rotate_dihedrals() change
dih_lib_only
model.restraints.make() make
dihedrals
model.rotate_dihedrals() change
distance_atoms
model.patch_ss_templates() guess | alignment.compare_structures() compare
distance_rsr_model
model.restraints.make() make
edat
environ.edat default | model.pick_hot_atoms() pick | model.write_data() write | model.energy() evaluate | model.optimize() optimize | model.debug_function() test | model.restraints.make() make | model.restraints.spline() approximate | alignment.compare_structures() compare
edit_align_codes
alignment.edit() edit
edit_file_ext
alignment.malign3d() align
em_density_format
density.read() read | density.grid_search() dock
em_fit_output_file
density.grid_search() dock
em_map_size
density.read() read
em_pdb_name
density.grid_search() dock
end_of_file
alignment.append() read
energy_data()
energy_data() create
energy_data.contact_shell
energy_data.contact_shell nonbond | energy_data.update_dynamic nonbond | model.optimize() optimize | model.restraints.make() make | Atomic density
energy_data.coulomb_switch
energy_data.contact_shell nonbond | energy_data.coulomb_switch Coulomb
energy_data.covalent_cys
energy_data.covalent_cys use
energy_data.dynamic_coulomb
energy_data.contact_shell nonbond | energy_data.dynamic_coulomb calculate | model.restraints.make() make
energy_data.dynamic_lennard
energy_data.contact_shell nonbond | energy_data.dynamic_lennard calculate | model.restraints.make() make
energy_data.dynamic_modeller
energy_data.dynamic_modeller calculate | energy_data.covalent_cys use | The group_restraints class: restraints
energy_data.dynamic_sphere
energy_data.contact_shell nonbond | energy_data.dynamic_sphere calculate | model.restraints.make() make
energy_data.excl_local
energy_data.excl_local exclude | model.restraints.make() make
energy_data.lennard_jones_switch
energy_data.contact_shell nonbond | energy_data.lennard_jones_switch Lennard-Jones
energy_data.nlogn_use
energy_data.nlogn_use select | model.optimize() optimize
energy_data.nonbonded_sel_atoms
energy_data.nonbonded_sel_atoms control | model.restraints.make() make | model.restraints.pick() pick
energy_data.radii_factor
energy_data.contact_shell nonbond | energy_data.radii_factor scale
energy_data.relative_dielectric
energy_data.relative_dielectric relative | Coulomb restraint
energy_data.update_dynamic
energy_data.contact_shell nonbond | energy_data.update_dynamic nonbond | model.optimize() optimize
env
automodel() prepare | allhmodel() prepare | loopmodel() prepare | model() create | alignment() create | profile() create | sequence_db() create | density() create
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.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
environ.edat default | energy_data() create
environ.io
environ.io default | io_data() create
environ.libs
environ.libs MODELLER | The libraries class: stereochemical
environ.principal_components()
environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_structures() compare | TOP to Python correspondence
environ.system()
environ.system() execute | TOP to Python correspondence
equilibrate
model.optimize() optimize | Molecular dynamics
equilibration
model.optimize() optimize
errors
log.level() Set
expand_control
alignment.expand() put
ext_tree
alignment.salign() align | Alignments using external restraints
extend_hot_spot
model.pick_hot_atoms() pick
fast_search
sequence_db.search() search
fast_search_cutoff
sequence_db.search() search
feature_weight
Features of proteins used
feature_weights
alignment.salign() align | Useful SALIGN information and
file
environ.principal_components() clustering | topology.append() append | topology.read() read | parameters.append() append | parameters.read() read | topology.write() write | model.read() read | model.write() write | model.write_data() write | model.write_pdb_xref() write | model.make_chains() Fetch | model.schedule.read() read | model.schedule.write() write | model.energy() evaluate | model.switch_trace() open | model.restraints.append() read | model.restraints.write() write | group_restraints.append() read | alignment.append() read | alignment.write() write | alignment.segment_matching() align | profile.read() read | profile.write() write | density.read() read | modfile.delete() delete | modfile.inquire() check
file naming
File naming
file types
File types
file_exists
modfile.inquire() check
file_ext
alignment.expand() put | alignment.segment_matching() align | modfile.default() generate
file_id
alignment.expand() put | alignment.segment_matching() align | modfile.default() generate
fit
model.superpose() superpose | alignment.write() write | alignment.align2d() align | alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used | Useful SALIGN information and
fit_atoms
alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used
fit_on_first
alignment.salign() align | Features of proteins used | Useful SALIGN information and
fit_pdbnam
alignment.salign() align | Features of proteins used
fix_offset
Alignments using external restraints
fix_offsets
alignment.salign() align | Alignments using external restraints
frequently asked questions
Frequently asked questions (FAQ)
gap_extension
model.pick_atoms() select
gap_function
alignment.salign() align | Alignment of protein sequences | Alignment of protein structures
gap_gap_score
alignment.salign() align | Gap penalties and correcting
gap_penalties_1d
alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.consensus() consensus | alignment.salign() align | Gap penalties and correcting | profile.read() read | profile.write() write | profile.scan() Compare | profile.build() Build | sequence_db.search() search | sequence_db.filter() cluster
gap_penalties_2d
alignment.align2d() align | alignment.salign() align | Alignment of protein structures
gap_penalties_3d
alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Features of proteins used
gap_penalty_1d
Gap penalties and correcting
gap_penalty_2d
Gap penalties and correcting
gap_penalty_3d
Gap penalties and correcting
gap_residue_score
alignment.salign() align | Gap penalties and correcting
gaps_in_target
profile.build() Build
grid_unit
model.write_data() write
group_restraints()
group_restraints() create | TOP to Python correspondence
group_restraints.append()
group_restraints() create | group_restraints.append() read | TOP to Python correspondence
id1
alignment.expand() put | modfile.default() generate
id2
alignment.expand() put | modfile.default() generate
improve_alignment
alignment.salign() align | Features of proteins used | Useful SALIGN information and
info.build_date
info.version return | info.build_date return
info.debug
info.debug returns
info.exe_type
info.exe_type return
info.time_mark()
info.time_mark() print | TOP to Python correspondence
info.version
info.version return
info.version_info
info.version return | info.version_info return
inifile
automodel() prepare | allhmodel() prepare | loopmodel() prepare
inimodel
loopmodel() prepare
init_velocities
model.optimize() optimize
initialize_xyz
model.build() build
input_profile_file
alignment.align2d() align
input_weights_file
alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.salign() align | Features of proteins used | Alignments using external restraints
installation
Installation
intersegment
model.restraints.make() make
io
environ.io default | model.read() read | model.generate_topology() generate | model.patch_ss_templates() guess | model.transfer_xyz() copy | model.restraints.make() make | alignment.append() read | alignment.check() check | alignment.edit() edit | alignment.describe() describe | alignment.align2d() align | alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | sequence_db.search() search
io_data()
io_data() create
io_data.atom_files_directory
Coordinate files and derivative | io_data.atom_files_directory search
io_data.hetatm
io_data() create | io_data.hetatm whether | Block (BLK) residues with
io_data.hydrogen
io_data() create | io_data.hydrogen whether
io_data.water
io_data() create | io_data.water whether
knowns
automodel() prepare | allhmodel() prepare | loopmodel() prepare
Lennard-Jones
Frequently asked questions (FAQ) | energy_data.contact_shell nonbond | energy_data.dynamic_lennard calculate | energy_data.lennard_jones_switch Lennard-Jones | Residues with defined topology, | Block (BLK) residues with | model.generate_topology() generate | model.optimize() optimize | Formats of the restraints | model.restraints.make() make | model.restraints.pick() pick | Function | Lennard-Jones restraint
libraries.parameters
libraries.parameters parameter
libraries.read_restyp()
Frequently asked questions (FAQ) | libraries.read_restyp() read | TOP to Python correspondence
libraries.topology
libraries.topology topology
library_schedule
automodel() prepare | allhmodel() prepare | loopmodel() prepare | model.schedule.make() create
local_alignment
alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | sequence_db.search() search
log.level()
log.level() Set | TOP to Python correspondence
log.minimal()
log.minimal() display
log.verbose()
environ() create | 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.loop.assess_methods
automodel() prepare
loopmodel.loop.ending_model
Loop optimization | loopmodel.loop.ending_model last | Loop modeling method
loopmodel.loop.md_level
loopmodel.loop.md_level control
loopmodel.loop.outputs
loopmodel.loop.outputs all
loopmodel.loop.starting_model
Loop optimization | loopmodel.loop.starting_model first | Loop modeling method
loopmodel.select_loop_atoms
Loop modeling method
loopmodel.select_loop_atoms()
loopmodel.select_loop_atoms() select
matrix_comparison
alignment.salign() align | Alignment of protein sequences
matrix_file
environ.dendrogram() clustering | environ.principal_components() clustering | alignment.id_table() calculate | alignment.compare_sequences() compare | alignment.compare_structures() compare
matrix_offset
alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | profile.read() read | profile.write() write | profile.scan() Compare | profile.build() Build | sequence_db.search() search | sequence_db.filter() cluster
max_aln_evalue
profile.scan() Compare | profile.build() Build
max_diff_res
sequence_db.filter() cluster
max_gap_length
alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.salign() align
max_gaps_match
alignment.compare_sequences() compare
max_iterations
automodel.max_var_iterations select | model.optimize() optimize
max_nonstdres
model.make_chains() Fetch
max_unaligned_res
sequence_db.filter() cluster
maximal_distance
model.restraints.make() make
md_return
model.optimize() optimize
md_time_step
model.optimize() optimize
mdl
model.res_num_from() residue | model.superpose() superpose | model.restraints.reindex() renumber | alignment.append_model() copy | alignment.compare_sequences() compare
memory
log.level() Set
method
Method for comparative protein
min_atom_shift
model.optimize() optimize
min_base_entries
alignment.edit() edit
min_loop_length
alignment.segment_matching() align
minimal_chain_length
model.make_chains() Fetch
minimal_resolution
model.make_chains() Fetch
minimal_stdres
model.make_chains() Fetch
minmax_db_seq_len
sequence_db.read() read
minmax_loop_length
model.pick_atoms() select
missing parameters
Frequently asked questions (FAQ) | Residues with defined topology,
mnch_lib
model.restraints.make() make
model()
model() create
model.assess_dope()
Changes since release 7v7 | automodel() prepare | model.assess_dope() assess
model.assess_ga341()
Changes since release 7v7 | automodel() prepare | model.seq_id sequence | model.assess_ga341() assess | model.assess_dope() assess
model.build()
Residues with defined topology, | model.generate_topology() generate | model.build() build | model.transfer_xyz() copy | TOP to Python correspondence | Flowchart of comparative modeling
model.color()
model.color() color | TOP to Python correspondence
model.debug_function()
model.debug_function() test | TOP to Python correspondence
model.energy()
Frequently asked questions (FAQ) | model.generate_topology() generate | model.energy() evaluate | model.optimize() optimize | model.debug_function() test | Formats of the restraints | model.symmetry.define() define | TOP to Python correspondence | Function | Flowchart of comparative modeling
model.generate_topology()
Frequently asked questions (FAQ) | model.read() read | model.generate_topology() generate | model.patch() patch | model.patch_ss_templates() guess | model.rotate_dihedrals() change | model.restraints.make() make | TOP to Python correspondence | Flowchart of comparative modeling
model.make_chains()
model.make_chains() Fetch | TOP to Python correspondence
model.make_region()
model.make_region() define | TOP to Python correspondence
model.mutate()
model.mutate() mutate | model.pick_atoms() select | TOP to Python correspondence
model.optimize()
automodel.max_var_iterations select | model.generate_topology() generate | model.pick_hot_atoms() pick | model.energy() evaluate | model.optimize() optimize | model.switch_trace() open | model.restraints.make() make | model.restraints.pick() pick | TOP to Python correspondence | Function | Flowchart of comparative modeling
model.orient()
model.orient() center | model.write_data() write | TOP to Python correspondence
model.patch()
Frequently asked questions (FAQ) | topology.append() append | parameters.append() append | model.generate_topology() generate | model.patch() patch | TOP to Python correspondence
model.patch_ss()
Frequently asked questions (FAQ) | model.patch_ss() guess | TOP to Python correspondence
model.patch_ss_templates()
Frequently asked questions (FAQ) | model.patch_ss_templates() guess | model.patch_ss() guess | TOP to Python correspondence | Flowchart of comparative modeling
model.pick_atoms()
Frequently asked questions (FAQ) | energy_data.nonbonded_sel_atoms control | Block (BLK) residues with | model.mutate() mutate | model.pick_atoms() select | model.superpose() superpose | model.restraints.make() make | TOP to Python correspondence
model.pick_hot_atoms()
energy_data.nonbonded_sel_atoms control | model.generate_topology() generate | model.pick_hot_atoms() pick | model.optimize() optimize | Formats of the restraints | TOP to Python correspondence | Function
model.randomize_xyz()
model.pick_atoms() select | model.randomize_xyz() randomize | model.schedule.make() create | TOP to Python correspondence | Flowchart of comparative modeling
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.rotate_dihedrals() change | model.make_chains() Fetch | model.restraints.condense() remove | TOP to Python correspondence | Flowchart of comparative modeling
model.rename_segments()
model.rename_segments() rename | TOP to Python correspondence
model.reorder_atoms()
model.reorder_atoms() standardize | TOP to Python correspondence
model.res_num_from()
model.res_num_from() residue | TOP to Python correspondence
model.restraints
model.restraints all
model.restraints.add()
Frequently asked questions (FAQ) | model.restraints.make() make | model.restraints.add() add | model.restraints.unpick() unselect | TOP to Python correspondence
model.restraints.append()
Frequently asked questions (FAQ) | model.restraints.append() read | model.restraints.write() write | TOP to Python correspondence | Flowchart of comparative modeling
model.restraints.clear()
model.restraints.clear() delete | model.restraints.append() read
model.restraints.condense()
Frequently asked questions (FAQ) | model.restraints.make() make | model.restraints.pick() pick | model.restraints.condense() remove | model.restraints.unpick() unselect | model.restraints.reindex() renumber | TOP to Python correspondence
model.restraints.make()
Frequently asked questions (FAQ) | Coordinate files and derivative | Residues with defined topology, | Block (BLK) residues with | model.patch_ss_templates() guess | model.pick_atoms() select | model.optimize() optimize | Static and dynamic restraints | model.restraints.make() make | model.restraints.pick() pick | model.restraints.spline() approximate | model.restraints.append() read | model.restraints.write() write | TOP to Python correspondence | Flowchart of comparative modeling
model.restraints.pick()
Frequently asked questions (FAQ) | model.pick_atoms() select | model.pick_hot_atoms() pick | model.schedule.make() create | model.schedule.read() read | model.symmetry.define() define | model.restraints.pick() pick | TOP to Python correspondence | Flowchart of comparative modeling
model.restraints.reindex()
model.restraints.reindex() renumber | TOP to Python correspondence
model.restraints.spline()
model.restraints.spline() approximate | TOP to Python correspondence
model.restraints.unpick()
Frequently asked questions (FAQ) | model.restraints.unpick() unselect | TOP to Python correspondence
model.restraints.unpick_all()
model.restraints.unpick_all() unselect | model.restraints.pick() pick
model.restraints.write()
model.restraints.write() write | TOP to Python correspondence | Flowchart of comparative modeling
model.rotate()
model.rotate() rotate | TOP to Python correspondence
model.rotate_dihedrals()
model.pick_atoms() select | model.rotate_dihedrals() change | TOP to Python correspondence
model.schedule.make()
automodel() prepare | model.schedule.make() create | model.schedule.step current | model.schedule.read() read | model.schedule.write() write | model.restraints.pick() pick | TOP to Python correspondence | Flowchart of comparative modeling
model.schedule.read()
model.schedule.make() create | model.schedule.read() read | model.schedule.write() write | TOP to Python correspondence
model.schedule.step
model.schedule.step current | model.energy() evaluate | model.optimize() optimize
model.schedule.write()
model.schedule.make() create | model.schedule.write() write | TOP to Python correspondence
model.seq_id
model.seq_id sequence | model.assess_ga341() assess
model.superpose()
Changes since release 7v7 | model.superpose() superpose | alignment.compare_structures() compare | TOP to Python correspondence
model.switch_trace()
model.optimize() optimize | model.switch_trace() open | TOP to Python correspondence
model.symmetry.define()
model.symmetry.define() define | TOP to Python correspondence
model.to_iupac()
model() create | model.to_iupac() standardize | TOP to Python correspondence
model.transfer_xyz()
automodel.cluster() cluster | Residues with defined topology, | model.seq_id sequence | model.generate_topology() generate | model.build() build | model.transfer_xyz() copy | alignment.malign3d() align | TOP to Python correspondence | Flowchart of comparative modeling
model.unbuild()
model.unbuild() undefine | TOP to Python correspondence
model.write()
model.write() write | TOP to Python correspondence | Flowchart of comparative modeling
model.write_data()
model.write_data() write | model.make_region() define | TOP to Python correspondence
model.write_pdb_xref()
model.write_pdb_xref() write | TOP to Python correspondence
model_format
model.read() read | model.write() write
model_segment
model.read() read | model.write_pdb_xref() write | Alignment file format
modfile.default()
Changes since release 7v7 | alignment.expand() put | modfile.default() generate
modfile.delete()
modfile.delete() delete | TOP to Python correspondence
modfile.inquire()
modfile.inquire() check | TOP to Python correspondence
molpdf
model.energy() evaluate | model.optimize() optimize | model.assess_ga341() assess | model.assess_dope() assess
n_prof_iterations
profile.read() read | profile.build() Build
n_subopt
alignment.salign() align | Sub-optimal alignments
neighbor_cutoff
model.write_data() write
no_ter
model.write() write | alignment.salign() align
normalize_pp_scores
alignment.salign() align | Useful SALIGN information and
normalize_profile
model.energy() evaluate
notes
log.level() Set
num_structures
density.grid_search() dock
number_of_steps
model.write_data() write | density.grid_search() dock
off_diagonal
alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | sequence_db.search() search
optimization_method
model.optimize() optimize
orient
model.write_data() write
output
model.write_data() write | model.energy() evaluate | model.optimize() optimize | model.symmetry.define() define | model.restraints.spline() approximate | alignment.compare_structures() compare | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Useful SALIGN information and | sequence_db.search() search | log.level() Set
output_alignments
profile.scan() Compare
output_cod_file
sequence_db.filter() cluster
output_directory
Output directory prefix | topology.write() write | model.write() write | model.write_pdb_xref() write | model.schedule.write() write | model.switch_trace() open | model.restraints.write() write | alignment.write() write | alignment.id_table() calculate | alignment.compare_sequences() compare | alignment.segment_matching() align
output_grp_file
sequence_db.filter() cluster
output_profile_file
alignment.align2d() align
output_score_file
profile.scan() Compare | profile.build() Build
output_scores
profile.scan() Compare | profile.build() Build
output_weights_file
alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.salign() align | Useful SALIGN information and
overhang
alignment.edit() edit | alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.align3d() align | alignment.malign3d() align | alignment.salign() align | Alignment of protein structures | sequence_db.search() search
overhang_auto_limit
alignment.salign() align | Alignment of protein structures
overhang_factor
alignment.salign() align | 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()
parameters.read() read | TOP to Python correspondence
parlib
automodel() prepare | allhmodel() prepare | loopmodel() prepare
patch_default
model.generate_topology() generate | model.patch() patch
pick_atoms_set
model.pick_atoms() select
pick_hot_cutoff
model.pick_hot_atoms() pick
prf
alignment.append_profile() add
probe_radius
model.write_data() write
profile()
profile() create
profile.build()
Changes since release 7v7 | The profile class: using | profile.read() read | profile.scan() Compare | profile.build() Build | The sequence_db class: using | sequence_db.read() read | sequence_db.write() write | TOP to Python correspondence
profile.read()
alignment.to_profile() convert | profile() create | profile.read() read | profile.to_alignment() profile | profile.scan() Compare | profile.build() Build | sequence_db.read() read | TOP to Python correspondence
profile.scan()
Changes since release 7v7 | The profile class: using | profile() create | profile.scan() Compare | 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
profile.read() read | profile.write() write | profile.scan() Compare
profile_list_file
profile.scan() Compare
program distribution
Distribution
program updates
MODELLER updates
psa_integration_step
model.write_data() write
pssm_weights_type
profile.scan() Compare
radii_factor
model.write_data() write
rand_seed
environ() create
read_profile
alignment.align2d() align
read_weights
alignment.align() align | alignment.align2d() align | alignment.consensus() consensus
reference_atom
model.superpose() superpose
reference_distance
model.superpose() superpose
refine_local
Changes since release 7v7 | model.superpose() superpose | alignment.compare_structures() compare
region_size
model.make_region() define
remove_gaps
alignment.append() read
renumber_residues
model.rename_segments() rename
res_types
model.pick_atoms() select
residue_grouping
model.restraints.make() make
residue_ids
Frequently asked questions (FAQ) | model.patch() patch | model.restraints.make() make
residue_span_range
energy_data.covalent_cys use | model.pick_hot_atoms() pick | model.energy() evaluate | model.optimize() optimize | model.restraints.make() make | model.restraints.pick() pick | model.restraints.spline() approximate
residue_span_sign
model.optimize() optimize | model.restraints.make() make
residue_type
model.patch() patch | model.mutate() mutate
resolution
density.grid_search() dock
restraint_group
model.restraints.make() make
restraint_parameters
model.restraints.make() make | model.restraints.add() add
restraint_sel_atoms
model.restraints.make() make | model.restraints.pick() pick
restraint_stdev
model.restraints.make() make
restraint_stdev2
model.restraints.make() make
restraint_type
Block (BLK) residues with | model.restraints.make() make | model.restraints.condense() remove
restraints_filter
model.restraints.pick() pick
restraints_format
model.restraints.write() write
restyp_lib_file
libraries.read_restyp() read
rewind_file
alignment.append() read
rms_cutoffs
model.superpose() superpose | alignment.compare_structures() compare | alignment.salign() align | Useful SALIGN information and
root_name
alignment.expand() put | alignment.segment_matching() align | modfile.default() generate
rotation_angle
model.rotate() rotate
rotation_axis
model.rotate() rotate
rotation_matrix
model.rotate() rotate
rr_file
alignment.compare_sequences() compare | alignment.align() align | alignment.align2d() align | alignment.malign() align | alignment.salign() align | Features of proteins used | Useful SALIGN information and | alignment.segment_matching() align | profile.read() read | profile.write() write | profile.scan() Compare | profile.build() Build | sequence_db.search() search | sequence_db.filter() cluster
schedule_scale
model.schedule.make() create | model.schedule.read() read | model.energy() evaluate
score_statistics
profile.scan() Compare
script file
Script file
sdb
profile.build() Build
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_report
alignment.segment_matching() align
segment_shift
alignment.segment_matching() align
segment_shifts
alignment.segment_matching() align
selection_from
model.pick_atoms() select
selection_mode
model.pick_atoms() select | model.pick_hot_atoms() pick
selection_search
model.pick_atoms() select
selection_segment
model.pick_atoms() select | Alignment file format
selection_slab
model.pick_atoms() select
selection_status
model.pick_atoms() select
seq_database_file
sequence_db.read() read | sequence_db.write() write
seq_database_format
sequence_db.read() read | sequence_db.write() write | sequence_db.filter() cluster
seqid_cut
sequence_db.filter() cluster
sequence
automodel() prepare | allhmodel() prepare | loopmodel() prepare | model.generate_topology() generate | model.rotate_dihedrals() change
sequence_db()
sequence_db() create
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()
profile.read() read | sequence_db() create | sequence_db.read() read | sequence_db.search() search | sequence_db.filter() cluster | TOP to Python correspondence
sequence_db.search()
Changes since release 7v7 | The sequence_db class: using | sequence_db.search() search | TOP to Python correspondence
sequence_db.write()
sequence_db.write() write | TOP to Python correspondence
sheet_h_bonds
model.restraints.make() make
signif_cutoff
sequence_db.search() search
similarity_flag
alignment.salign() align | Features of proteins used | Useful SALIGN information and
smooth_prof_weight
alignment.align() align | alignment.align2d() align | alignment.salign() align
smoothing_window
model.energy() evaluate
sphere_center
model.pick_atoms() select
sphere_radius
model.pick_atoms() select
spline_dx
model.restraints.make() make | model.restraints.spline() approximate
spline_min_points
model.restraints.make() make | model.restraints.spline() approximate
spline_on_site
model.restraints.make() make
spline_range
model.restraints.make() make | model.restraints.spline() approximate
spline_select
model.restraints.spline() approximate
start_type
density.grid_search() dock
statistical potential
Loop modeling method
structure_types
model.make_chains() Fetch
submodel
topology.make() make
subopt_offset
alignment.align2d() align | alignment.salign() align | Sub-optimal alignments
substitution
alignment.salign() align
summary_file
profile.scan() Compare
superpose_refine
model.superpose() superpose
surftyp
model.write_data() write
swap_atoms_in_res
model.superpose() superpose
symmetry_weight
model.symmetry.define() define
target_profile_file
profile.scan() Compare
temperature
model.optimize() optimize | density.grid_search() dock
toplib
automodel() prepare | loopmodel() prepare
topology.append()
libraries.topology topology | topology.append() append | topology.read() read | model.rotate_dihedrals() change | TOP to Python correspondence
topology.clear()
topology.append() append | topology.clear() clear | topology.read() read
topology.make()
Changes since release 7v7 | topology.append() append | topology.make() make | topology.submodel select | topology.write() write | TOP to Python correspondence
topology.read()
topology.read() read | topology.submodel select | TOP to Python correspondence
topology.submodel
Frequently asked questions (FAQ) | automodel() prepare | 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
topology.write()
topology.write() write | TOP to Python correspondence
topology_model
automodel() prepare | loopmodel() prepare
trace_output
model.optimize() optimize | model.switch_trace() open
translate_type
density.grid_search() dock
translation
model.rotate() rotate
tutorial
Tutorial on using MODELLER
variability_file
alignment.compare_sequences() compare
viol_report_cut
model.pick_hot_atoms() pick | model.energy() evaluate
viol_report_cut2
model.energy() evaluate
voxel_size
density.grid_search() dock
warnings
log.level() Set
weigh_sequences
alignment.align() align | alignment.align2d() align
weights_type
alignment.salign() align | Features of proteins used
write_all_atoms
model.write() write
write_fit
alignment.malign3d() align | alignment.salign() align | Features of proteins used | Useful SALIGN information and
write_profile
alignment.align2d() align
write_summary
profile.scan() Compare
write_weights
alignment.align() align | alignment.align2d() align | alignment.consensus() consensus | alignment.salign() align | Useful SALIGN information and
write_whole_pdb
alignment.malign3d() align | alignment.salign() align | Useful SALIGN information and



Ben Webb 2005-04-21