Contents

• List of Figures
• List of Tables
• Introduction
  • What is MODELLER?
  • MODELLER bibliography
  • Obtaining and installing the program
  • Bug reports
  • Method for comparative protein structure modeling by MODELLER
  • Using MODELLER for comparative modeling
    • Preparing input files
    • Running MODELLER
  
  
• Automated comparative modeling with automodel
  • Simple usage
  • More advanced usage
    • Including water molecules, HETATM residues, and hydrogen atoms
    • Changing the default optimization and refinement protocol
    • Getting a very fast and approximate model
    • Building a model from multiple templates
    • Building an all hydrogen model
    • Refining only part of the model
    • Including disulfide bridges
    • Generating new-style PDBx/mmCIF outputs
    • Providing your own restraints file
    • Using your own initial model
    • Adding additional restraints to the defaults
    • Building multi-chain models
    • Residues and chains in multi-chain models
    • Accessing output data after modeling is complete
    • Fully automated alignment and modeling
  • Loop optimization
    • Automatic loop refinement after model building
    • Defining loop regions for refinement
    • Refining an existing PDB file
  
  
• Frequently asked questions and history
  • Frequently asked questions (FAQ) and examples
  • MODELLER updates
    • Changes since release 9.20
    • Changes since release 9.19
  
  
• Comparative modeling class reference
  • automodel reference
    • automodel() — prepare to build one or more comparative models
    • automodel.library_schedule — select optimization schedule
    • automodel.md_level — control the model refinement level
    • automodel.outputs — all output data for generated models
    • automodel.rand_method — control initial model randomization
    • automodel.generate_method — control initial model generation
    • automodel.max_var_iterations — select length of optimizations
    • automodel.repeat_optimization — number of times to repeat optimization
    • automodel.max_molpdf — objective function cutoff
    • automodel.initial_malign3d — initial template alignment
    • automodel.starting_model — first model to build
    • automodel.ending_model — last model to build
    • automodel.final_malign3d — final template-model alignment
    • automodel.write_intermediates — write intermediate files during optimization
    • automodel.trace_output — control optimization output
    • automodel.max_ca_ca_distance — Distance cutoff for CA-CA homology-derived restraints
    • automodel.max_n_o_distance — Distance cutoff for N-O homology-derived restraints
    • automodel.max_sc_mc_distance — Distance cutoff for sidechain-mainchain homology-derived restraints
    • automodel.max_sc_sc_distance — Distance cutoff for sidechain-sidechain homology-derived restraints
    • automodel.set_output_model_format() — set format for output models
    • automodel.get_optimize_actions() — get actions to carry out during the initial optimization
    • automodel.get_refine_actions() — get actions to carry out during the refinement
    • automodel.select_atoms() — select region for optimization
    • automodel.auto_align() — generate an automatic initial alignment
    • automodel.very_fast() — request rapid optimization
    • automodel.make() — build all models
    • automodel.cluster() — cluster all built models
    • automodel.special_restraints() — add additional restraints
    • automodel.nonstd_restraints() — add restraints on ligands
    • automodel.special_patches() — add additional patches to the topology
    • automodel.user_after_single_model() — analyze or refine each model
    • automodel.get_model_filename() — get the model PDB/mmCIF name
    • automodel.use_parallel_job() — parallelize model building
    • automodel.guess_atom_types() — automatically assign CHARMM atom types
    • automodel.guess_atom_type() — automatically assign CHARMM atom type
  • allhmodel reference
    • allhmodel() — prepare to build all-hydrogen models
  • loopmodel reference
    • loopmodel() — prepare to build models with loop refinement
    • loopmodel.loop.md_level — control the loop model refinement level
    • loopmodel.loop.max_var_iterations — select length of optimizations
    • loopmodel.loop.library_schedule — select optimization schedule
    • loopmodel.loop.starting_model — first loop model to build
    • loopmodel.loop.ending_model — last loop model to build
    • loopmodel.loop.write_selection_only — write PDB/mmCIFs containing only the loops
    • loopmodel.loop.write_defined_only — only write non-loop atoms present in the input model
    • loopmodel.loop.outputs — all output data for generated loop models
    • loopmodel.select_loop_atoms() — select region for loop optimization
    • loopmodel.get_loop_model_filename() — get the model PDB/mmCIF name
    • loopmodel.user_after_single_loop_model() — analyze or refine each loop model
    • loopmodel.read_potential() — read in the loop modeling potential
    • loopmodel.build_ini_loop() — create the initial conformation of the loop
  • dope_loopmodel reference
    • dope_loopmodel() — prepare to build models with DOPE loop refinement
  • dopehr_loopmodel reference
  
  
• MODELLER general reference
  • Miscellaneous rules and features of MODELLER
    • MODELLER system
    • Controlling breakpoints and the amount of output
    • File naming
    • File types
  • Stereochemical parameters and molecular topology
    • Modeling residues with non-existing or incomplete entries in the topology and parameter libraries
  • Spatial restraints
    • Specification of restraints
    • Specification of pseudo atoms
    • Excluded pairs
    • Rigid bodies
    • Symmetry restraints
  
  
• MODELLER command reference
  • 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 $P(r)$ 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
    • 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
  
  
• MODELLER low-level programming
  • User-defined features and restraint forms
    • User-defined feature types
    • User-defined restraint forms
    • User-defined energy terms
  • MODELLER programming interface (API)
  
  
• Methods
  • Dynamic programming for sequence and structure comparison and searching
    • Pairwise comparison
    • Variable gap penalty
    • Local versus global alignment
    • Similarity versus distance scores
    • Multiple comparisons
  • Optimization of the objective function by MODELLER
    • Function
    • Optimizers
  • Equations used in the derivation of the molecular pdf
    • Features and their derivatives
    • Restraints and their derivatives
  • Flowchart of comparative modeling by MODELLER
  • Loop modeling method
  
  
• File formats
  • Alignment file (PIR)
  • Restraints file
    • Restraints
    • Excluded pairs
    • Pseudo atoms
    • Symmetry restraints
    • Rigid bodies
  • Profile file
  • Binary files
  
  
• Converting TOP scripts from old MODELLER versions
  • Running old scripts unchanged
  • Converting TOP scripts to Python
    • TOP commands and variables
    • TOP models and alignments
    • TOP to Python correspondence
  
  
• Bibliography
• Index