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Contents
- 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()
- Changes since release 8v0
| 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
- Simple usage
| 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()
- Simple usage
| 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
- Simple usage
| 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
- chains_num
- density.grid_search() dock
- 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.read() read
- 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
- 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
| model.write_data() write
- 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
| group_restraints() 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()
- Frequently asked questions (FAQ)
| Simple usage
| 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
- 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
- exit_stage
- automodel.make() build
- 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
- Simple usage
| 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
| model.assess_dope() assess
| Formats of the restraints
| model.restraints.make() make
| model.restraints.pick() pick
| Function
| Lennard-Jones restraint
- libraries.parameters
- libraries.parameters parameter
- 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()
- loopmodel.select_loop_atoms() select
| Loop modeling method
- 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
| model.assess_dope() assess
| 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)
| Changes since release 8v0
| 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()
- energy_data.radii_factor scale
| 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
- 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
- Changes since release 8v0
| 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.read() read
- 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
- Changes since release 8v0
| environ() create
- 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
| model.assess_dope() assess
- 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
| sequence_db.search() search
- 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
- 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)
| Changes since release 8v0
| 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.read() read
- 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
2005-06-20