MODELLER command reference

Subsections

Key for command descriptions
The environ class: MODELLER environment
- environ() — create a new MODELLER environment
- environ.io — default input parameters
- environ.edat — default objective function parameters
- environ.libs — MODELLER libraries
- environ.schedule_scale — energy function scaling factors
- environ.dendrogram() — clustering
- environ.principal_components() — clustering
- environ.system() — execute system command
- environ.make_pssmdb() — Create a database of PSSMs given a list of profiles
The energy_data class: objective function parameters
- energy_data() — create a new set of objective function parameters
- energy_data.contact_shell — nonbond distance cutoff
- energy_data.update_dynamic — nonbond recalculation threshold
- energy_data.sphere_stdv — soft-sphere standard deviation
- energy_data.dynamic_sphere — calculate soft-sphere overlap restraints
- energy_data.dynamic_lennard — calculate Lennard-Jones restraints
- energy_data.dynamic_coulomb — calculate Coulomb restraints
- energy_data.dynamic_modeller — calculate non-bonded spline restraints
- energy_data.excl_local — exclude certain local pairs of atoms
- energy_data.radii_factor — scale atomic radii
- energy_data.lennard_jones_switch — Lennard-Jones switching parameters
- energy_data.coulomb_switch — Coulomb switching parameters
- energy_data.relative_dielectric — relative dielectric
- energy_data.covalent_cys — use disulfide bridges in residue distance
- energy_data.nonbonded_sel_atoms — control interaction with picked atoms
- energy_data.nlogn_use — select non-bond list generation algorithm
- energy_data.max_nlogn_grid_cells — maximum number of grid cells for NlogN nonbond pairs routine
- energy_data.energy_terms — user-defined global energy terms
The io_data class: coordinate file input parameters
- io_data() — create a new input parameters object
- io_data.hetatm — whether to read HETATM records
- io_data.hydrogen — whether to read hydrogen atoms
- io_data.water — whether to read water molecules
- io_data.convert_modres — whether to convert modified residues
- io_data.atom_files_directory — search path for coordinate files
The Libraries class: stereochemical parameters and molecular topology
- Libraries.topology — topology library information
- Libraries.parameters — parameter library information
- Topology.append() — append residue topology library
- Topology.clear() — clear residue topology library
- Topology.read() — read residue topology library
- Parameters.append() — append parameters library
- Parameters.clear() — clear parameters library
- Parameters.read() — read parameters library
- Topology.make() — make a subset topology library
- Topology.submodel — select topology model type
- Topology.write() — write residue topology library
The model class: handling of atomic coordinates, and model building
- model() — create a new 3D model
- model.seq_id — sequence identity between the model and templates
- model.resolution — resolution of protein structure
- model.last_energy — last objective function value
- model.remark — text remark(s)
- model.restraints — all static restraints which act on the model
- model.group_restraints — all restraints which act on atom groups
- model.atoms — all atoms in the model
- model.point() — return a point in Cartesian space
- model.atom_range() — return a subset of all atoms
- model.residue_range() — return a subset of all residues
- model.get_insertions() — return a list of all insertions
- model.get_deletions() — return a list of all deletions
- model.loops() — return a list of all loops
- model.read() — read coordinates for MODEL
- model.build_sequence() — build model from a sequence of one-letter codes
- model.write() — write MODEL
- model.clear_topology() — clear model topology
- model.generate_topology() — generate MODEL topology
- model.make_valid_pdb_coordinates() — make coordinates fit in PDB format
- model.write_psf() — write molecular topology to PSF file
- model.patch() — patch MODEL topology
- model.patch_ss_templates() — guess MODEL disulfides from templates
- model.patch_ss() — guess MODEL disulfides from model structure
- model.build() — build MODEL coordinates from topology
- model.transfer_xyz() — copy templates' coordinates to MODEL
- model.res_num_from() — residue numbers from MODEL2 to MODEL
- model.rename_segments() — rename MODEL segments
- model.to_iupac() — standardize certain dihedral angles
- model.reorder_atoms() — standardize order of MODEL atoms
- model.orient() — center and orient MODEL
- model.write_data() — write derivative model data
- model.make_region() — define a random surface patch of atoms
- model.color() — color MODEL according to alignment
- model.make_chains() — Fetch sequences from PDB file
- model.saxs_intens() — Calculate SAXS intensity from model
- model.saxs_pr() — Calculate of model
- model.saxs_chifun() — Calculate SAXS score chi from model
- model.assess_ga341() — assess a model with the GA341 method
- model.assess_normalized_dope() — assess a model with the normalized DOPE method
- model.get_normalized_dope_profile() — get per-residue normalized DOPE profile
The Restraints class: static restraints
- Restraints.rigid_bodies — all rigid bodies
- Restraints.pseudo_atoms — all pseudo atoms
- Restraints.excluded_pairs — all excluded pairs
- Restraints.nonbonded_pairs — all nonbonded pairs
- Restraints.symmetry — all symmetry restraints
- Restraints.symmetry.report() — report violated symmetry restraints
- Restraints.make() — make restraints
- Restraints.make_distance() — make distance restraints
- Restraints.unpick_all() — unselect all restraints
- Restraints.clear() — delete all restraints
- Restraints.pick() — pick restraints for selected atoms
- Restraints.unpick_redundant() — unselect redundant restraints
- Restraints.remove_unpicked() — remove unselected restraints
- Restraints.condense() — remove unselected or redundant restraints
- Restraints.add() — add restraint
- Restraints.unpick() — unselect restraints
- Restraints.reindex() — renumber model restraints using another model
- Restraints.spline() — approximate restraints by splines
- Restraints.append() — read spatial restraints
- Restraints.write() — write spatial restraints
The secondary_structure module: secondary structure restraints
- alpha() — make an α -helix
- strand() — make a β -strand
- sheet() — make a β -sheet
The selection class: handling of sets of atom coordinates
- selection() — create a new selection
- selection.add() — add objects to selection
- selection.extend_by_residue() — extend selection by residue
- selection.by_residue() — make sure all residues are fully selected
- selection.select_sphere() — select all atoms within radius
- selection.only_mainchain() — select only mainchain atoms
- selection.only_sidechain() — select only sidechain atoms
- selection.only_atom_types() — select only atoms of given types
- selection.only_residue_types() — select only atoms of given residue type
- selection.only_std_residues() — select only standard residues
- selection.only_no_topology() — select only residues without topology
- selection.only_het_residues() — select only HETATM residues
- selection.only_water_residues() — select only water residues
- selection.only_defined() — select only atoms with defined coordinates
- selection.write() — write selection coordinates to a file
- selection.translate() — translate all coordinates
- selection.rotate_origin() — rotate coordinates about origin
- selection.rotate_mass_center() — rotate coordinates about mass center
- selection.transform() — transform coordinates with a matrix
- selection.mutate() — mutate selected residues
- selection.randomize_xyz() — randomize selected coordinates
- selection.superpose() — superpose model on selection given alignment
- selection.rotate_dihedrals() — change dihedral angles
- selection.unbuild() — undefine coordinates
- selection.hot_atoms() — atoms violating restraints
- selection.energy() — evaluate atom selection given restraints
- selection.debug_function() — test code self-consistency
- selection.assess_dope() — assess a model selection with the DOPE method
- selection.assess_dopehr() — assess a model with the DOPE-HR method
- selection.get_dope_profile() — get per-residue DOPE profile
- selection.get_dopehr_profile() — get per-residue DOPE-HR profile
- selection.assess() — assess a model selection
The physical module: contributions to the objective function
- physical.values() — create a new set of physical values
The optimizers module: optimization of the model
- conjugate_gradients() — optimize atoms given restraints, with CG
- quasi_newton() — optimize atoms with quasi-Newton minimization
- molecular_dynamics() — optimize atoms given restraints, with MD
- actions.write_structure() — write out the model coordinates
- actions.trace() — write out optimization energies, etc
- actions.charmm_trajectory() — write out a CHARMM trajectory
- User-defined optimizers
The schedule class: variable target function optimization
- schedule() — create a new schedule
- schedule.make_for_model() — trim a schedule for a model
- schedule.write() — write optimization schedule
The group_restraints class: restraints on atom groups
- group_restraints() — create a new set of group restraints
- group_restraints.append() — read group restraint parameters
The gbsa module: implicit solvation
- gbsa.Scorer() — create a new scorer to evaluate GB/SA energies
SOAP potentials
- soap_loop.Scorer() — create a new scorer to evaluate SOAP-Loop energies
- soap_peptide.Scorer() — create a new scorer to evaluate SOAP-Peptide energies
- soap_pp.PairScorer() — create a new scorer to evaluate SOAP-PP pairwise energies
- soap_pp.AtomScorer() — create a new scorer to evaluate SOAP-PP atomistic energies
- soap_pp.Assessor() — assess with all components of the SOAP-PP score
- soap_protein_od.Scorer() — create a new scorer to evaluate SOAP-Protein-OD energies
The alignment class: comparison of sequences and structures
- alignment() — create a new alignment
- alignment.comments — alignment file comments
- alignment.positions — list of residue-residue alignment positions (including gaps)
- alignment.append() — read sequences and/or their alignment
- alignment.clear() — delete all sequences from the alignment
- alignment.read_one() — read sequences one by one from a file
- alignment.check_structure_structure() — check template structure superpositions
- alignment.check_sequence_structure() — check sequence/structure alignment for sanity
- alignment.check() — check alignment for modeling
- alignment.compare_with() — compare two alignments
- alignment.append_model() — copy model sequence and coordinates to alignment
- alignment.append_sequence() — add a sequence from one-letter codes
- alignment.append_profile() — add profile sequences to the alignment
- alignment.write() — write sequences and/or their alignment
- alignment.edit() — edit overhangs in alignment
- alignment.describe() — describe proteins
- alignment.id_table() — calculate percentage sequence identities
- alignment.compare_sequences() — compare sequences in alignment
- alignment.align() — align two (blocks of) sequences
- alignment.align2d() — align sequences with structures
- alignment.malign() — align two or more sequences
- alignment.consensus() — consensus sequence alignment
- alignment.compare_structures() — compare 3D structures given alignment
- alignment.align3d() — align two structures
- alignment.malign3d() — align two or more structures
- alignment.salign() — align two or more sequences/structures of proteins
  - Features of proteins used for alignment
  - Alignment of protein sequences
  - Alignment of protein structures with sequences
  - Alignment of protein structures
  - Sub-optimal alignments
  - Alignments using external restraints
  - Gap penalties and correcting for gaps
  - Useful SALIGN information and commands
- alignment.get_suboptimals() — parse suboptimal alignments file
- alignment.to_profile() — convert alignment to profile format
- alignment.segment_matching() — align segments
The Sequence class: a single sequence within an alignment
- Sequence.range — residue range
- Sequence.code — alignment code
- Sequence.atom_file — PDB file name
- Sequence.source — source organism
- Sequence.name — protein name
- Sequence.prottyp — protein sequence type
- Sequence.resolution — structure resolution
- Sequence.rfactor — R factor
- Sequence.residues — list of all residues in the sequence
- Sequence.chains — list of all chains in the sequence
- Sequence.transfer_res_prop() — transfer residue properties
- Sequence.get_num_equiv() — get number of equivalences
- Sequence.get_sequence_identity() — get sequence identity
The Structure class: a template structure within an alignment
- Structure.write() — write out PDB file
- Structure.reread() — reread coordinates from the atom file
- Structure.read() — read coordinates from a PDB file
The Chain class: a single chain in a model or alignment
- Chain.name — chain ID
- Chain.residues — all residues in the chain
- Chain.atoms — all atoms in the chain
- Chain.filter() — check if this chain passes all criteria
- Chain.write() — write out chain sequence to an alignment file
- Chain.atom_file_and_code() — get suitable names for this chain
- Chain.join() — join other chain(s) onto this one
The Residue class: a single residue in a model or alignment
- Residue.name — internal (CHARMM) residue type name
- Residue.pdb_name — PDB (IUPAC) type name
- Residue.code — One-letter residue type code
- Residue.hetatm — HETATM indicator
- Residue.index — internal integer index
- Residue.num — PDB-style residue number
- Residue.curvature — Mainchain curvature
- Residue.atoms — all atoms in the residue
- Residue.chain — chain object
- Residue.phi — φ dihedral angle
- Residue.psi — ψ dihedral angle
- Residue.omega — ω dihedral angle
- Residue.alpha — α dihedral angle
- Residue.chi1 — χ₁ dihedral angle
- Residue.chi2 — χ₂ dihedral angle
- Residue.chi3 — χ₃ dihedral angle
- Residue.chi4 — χ₄ dihedral angle
- Residue.chi5 — χ₅ dihedral angle
- Residue.get_aligned_residue() — get aligned residue in another sequence
- Residue.add_leading_gaps() — add gap(s) before this residue
- Residue.add_trailing_gaps() — add gap(s) after this residue
- Residue.remove_leading_gaps() — remove gap(s) before this residue
- Residue.remove_trailing_gaps() — remove gap(s) after this residue
- Residue.get_leading_gaps() — get number of gaps before this residue
- Residue.get_trailing_gaps() — get number of gaps after this residue
The Dihedral class: a single dihedral in a model or alignment
- Dihedral.value — current value in degrees
- Dihedral.atoms — atoms defining the angle
- Dihedral.dihclass — integer dihedral class
The Point class: a point in Cartesian space
- Point.x — x coordinate
- Point.select_sphere() — select all atoms within radius
The Atom class: a single atom in a model or structure
- Atom.dvx — objective function derivative
- Atom.vx — x component of velocity
- Atom.biso — isotropic temperature factor
- Atom.accessibility — atomic accessibility
- Atom.occ — occupancy
- Atom.charge — electrostatic charge
- Atom.mass — mass
- Atom.name — PDB name
- Atom.type — CHARMM atom type
- Atom.residue — residue object
- Atom.get_equivalent_atom() — get equivalent atom in another residue
The AtomType class: a CHARMM atom type
- AtomType.name — CHARMM name
- AtomType.mass — atomic mass
- AtomType.element — element
The EnergyProfile class: a per-residue energy profile
- EnergyProfile.min_rms — minimal RMS violation
- EnergyProfile.heavy_rms — heavy RMS violation
- EnergyProfile.get_normalized() — get a normalized energy profile
- EnergyProfile.get_smoothed() — get a smoothed energy profile
- EnergyProfile.write_to_file() — write to file
The profile class: using sequence profiles
- profile() — create a new profile
- profile.read() — read a profile of a sequence
- profile.write() — write a profile
- profile.to_alignment() — profile to alignment
- profile.scan() — Compare a target profile against a database of profiles
- profile.build() — Build a profile for a given sequence or alignment
- pssmdb() — create a new PSSM database
- pssmdb.read() — read a PSSM database from a file
The sequence_db class: using sequence databases
- sequence_db() — create a new sequence database
- sequence_db.read() — read a database of sequences
- sequence_db.close() — close an open database
- sequence_db.write() — write a database of sequences
- sequence_db.convert() — convert a database to binary format
- sequence_db.search() — search for similar sequences
- sequence_db.filter() — cluster sequences by sequence-identity
The density class: handling electron microscopy density data
- density() — create a new density map
- density.resolution — Map resolution
- density.sigma_factor — Sigma factor
- density.voxel_size — Map voxel size
- density.px — Origin of the map
- density.py — Origin of the map
- density.pz — Origin of the map
- density.grid — Density values
- density.read() — read an EM (electron microscopy) density map file
- density.grid_search() — dock a structure into an EM (electron microscopy) density map
The saxsdata class: using small-angle X-ray (SAXS) data
- saxsdata() — create a new saxsdata structure
- saxsdata.ini_saxs() — Initialization of SAXS data
- saxsdata.saxs_read() — Read in SAXS data
- saxsdata.saxs_pr_read() — Read in P(r) data
The info object: obtaining information about the MODELLER build
- info.version — the full MODELLER version number
- info.version_info — the version number, as a tuple
- info.build_date — the date this binary was built
- info.exe_type — the executable type of this binary
- info.debug — this binary's debug flag
- info.bindir — MODELLER binary directory
- info.time_mark() — print current date, time, and CPU time
- info.jobname — name of the current job
The log object: controlling the amount of output
- log.level() — Set all log output levels
- log.none() — display no log output
- log.minimal() — display minimal log output
- log.verbose() — display verbose log output
- log.very_verbose() — display verbose log output, and dynamic memory information
The modfile module: handling of files
- modfile.default() — generate an ‘automatic’ filename
- modfile.delete() — delete a file
- modfile.inquire() — check if file exists
- modfile.File() — open a handle to a MODELLER file
The scripts module: utility scripts
- cispeptide() — creates cis-peptide stereochemical restraints
- complete_pdb() — read a PDB or mmCIF file, and fill in any missing atoms
The salign module: high-level usage of SALIGN
- iterative_structural_align() — obtain the best structural alignment
Parallel job support
- job() — create a new parallel job
- sge_pe_job() — create a job using all Sun GridEngine (SGE) slave processes
- sge_qsub_job() — create a job which can be expanded with Sun GridEngine 'qsub'
- job.slave_startup_commands — Slave startup commands
- job.queue_task() — submit a task to run within the job
- job.run_all_tasks() — run all queued tasks, and return results
- job.yield_tasks_unordered() — run all queued tasks, and yield unordered results
- job.start() — start all slaves for message-passing
- Communicator.send_data() — send data
- Communicator.get_data() — get data
- slave.run_cmd() — run a command on the slave
- local_slave() — create a slave running on the local machine
- sge_pe_slave() — create a slave running on a Sun GridEngine parallel environment slave node
- sge_qsub_slave() — create a 'qsub' slave running on a Sun GridEngine node
- ssh_slave() — create a slave on a remote host accessed via ssh

Automatic builds 2018-12-06