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
    • Providing your own restraints file
    • Using your own initial model
    • Adding additional restraints to the defaults
    • Building multi-chain models with symmetry
    • 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 9v4
    • Changes since release 9v3
  
  
• 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.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 name
    • automodel.use_parallel_job() -- parallelize model building
  • 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.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 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.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.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.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
  • The Restraints class: static restraints
    • Restraints.rigid_bodies -- all rigid bodies
    • Restraints.pseudo_atoms -- all pseudo atoms
    • Restraints.excluded_pairs -- all excluded 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
  • 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
  • The alignment class: comparison of sequences and structures
    • alignment() -- create a new alignment
    • alignment.comments -- alignment file comments
    • 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.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 atom 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
  • 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.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.occ -- occupancy
    • Atom.charge -- electrostatic charge
    • Atom.mass -- mass
    • Atom.name -- PDB name
    • Atom.element -- Element symbol
    • Atom.residue -- residue object
  • 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.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.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 file, and fill in any missing atoms
  • 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.queue_task() -- submit a task to run within the job
    • job.run_all_tasks() -- run all queued tasks, and return 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