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.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 $\alpha$ -helix
- strand() -- make a $\beta$ -strand
- sheet() -- make a $\beta$ -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_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 -- $\phi$ dihedral angle
- Residue.psi -- $\psi$ dihedral angle
- Residue.omega -- $\omega$ dihedral angle
- Residue.alpha -- $\alpha$ dihedral angle
- Residue.chi1 -- $\chi _1$ dihedral angle
- Residue.chi2 -- $\chi _2$ dihedral angle
- Residue.chi3 -- $\chi _3$ dihedral angle
- Residue.chi4 -- $\chi _4$ dihedral angle
- Residue.chi5 -- $\chi _5$ 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 2014-07-26