Contents

• List of Figures
• List of Tables
• Introduction
  • What is MODELLER?
  • MODELLER bibliography
  • Distribution
  • Installation
  • Bug reports
  • Method for comparative protein structure modeling by MODELLER
  • Tutorial on using MODELLER for comparative modeling
    • Preparing input files
    • Running MODELLER
  • Frequently asked questions (FAQ) and examples
  • MODELLER updates
    • Changes since release 7v7
    • Changes since release 6v2
    • Changes between releases 4 and 6v2
  
  
• Automated comparative modeling with automodel
  • Simple usage
  • More advanced usage
    • Including water molecules, HETATM residues, and hydrogen atoms
    • Getting a very fast and approximate model
    • Building an all hydrogen model
    • Refining only part of the model
    • Providing your own restraints file
    • Using your own initial model
    • Adding additional restraints to the defaults
    • Fully automated alignment and modeling
    • Loop optimization
  • automodel reference
    • automodel() -- prepare to build one or more comparative models
    • 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.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.special_patches() -- add additional patches to the topology
    • automodel.user_after_single_model() -- analyze or refine each model
  • 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.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
  
  
• MODELLER command reference
  • Miscellaneous rules and features of MODELLER
    • MODELLER system
    • Controlling breakpoints and the amount of output
    • File naming
    • File types
    • 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.dendrogram() -- clustering
    • environ.principal_components() -- clustering
    • environ.system() -- execute system command
  • 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.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
  • 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
    • Modeling residues with non-existing or incomplete entries in the topology and parameter libraries
    • libraries.read_restyp() -- read residue type library
    • 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.restraints -- all restraints which act on the model
    • model.read() -- read coordinates for MODEL
    • model.write() -- write MODEL
    • model.generate_topology() -- generate MODEL topology
    • model.patch() -- patch MODEL topology
    • model.patch_ss_templates() -- guess MODEL disulfides from templates
    • model.patch_ss() -- guess MODEL disulfides from model structure
    • model.mutate() -- mutate selected MODEL residues
    • model.build() -- build MODEL coordinates from topology
    • model.unbuild() -- undefine MODEL coordinates
    • 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.pick_atoms() -- select atoms in MODEL
    • model.pick_hot_atoms() -- pick atoms violating restraints
    • model.randomize_xyz() -- randomize MODEL coordinates
    • model.to_iupac() -- standardize certain dihedral angles
    • model.reorder_atoms() -- standardize order of MODEL atoms
    • model.rotate_dihedrals() -- change dihedral angles
    • model.orient() -- center and orient MODEL
    • model.rotate() -- rotate and translate MODEL
    • model.write_data() -- write derivative MODEL data
    • model.write_pdb_xref() -- write residue number/index correspondence
    • model.make_region() -- define a random surface patch of atoms
    • model.color() -- color MODEL according to alignment
    • model.superpose() -- superpose MODEL2 on MODEL given alignment
    • model.make_chains() -- Fetch sequences from PDB file
    • model.schedule.make() -- create optimization schedule
    • model.schedule.step -- current optimization schedule step
    • model.schedule.read() -- read optimization schedule
    • model.schedule.write() -- write optimization schedule
    • model.energy() -- evaluate MODEL given restraints
    • model.optimize() -- optimize MODEL given restraints
    • model.switch_trace() -- open new optimization trace file
    • model.debug_function() -- test code self-consistency
    • model.assess_ga341() -- assess a model with the GA341 method
    • model.assess_dope() -- assess a model with the DOPE method
  • Calculation of spatial restraints
    • Specification of restraints
    • Specification of pseudo atoms
    • model.restraints.make() -- make restraints
    • model.symmetry.define() -- define similar segments
    • model.restraints.unpick_all() -- unselect all restraints
    • model.restraints.clear() -- delete all restraints
    • model.restraints.pick() -- pick restraints for selected atoms
    • model.restraints.condense() -- remove unselected restraints
    • model.restraints.add() -- add restraint
    • model.restraints.unpick() -- unselect restraint
    • model.restraints.reindex() -- renumber MODEL2 restraints for MODEL
    • model.restraints.spline() -- approximate restraints by splines
    • model.restraints.append() -- read spatial restraints
    • model.restraints.write() -- write spatial restraints
  • 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 alignment class: comparison of sequences and structures
    • Alignment file format
    • alignment() -- create a new alignment
    • alignment.append() -- read sequences and/or their alignment
    • alignment.clear() -- delete all sequences from the alignment
    • alignment.check() -- check alignment for modeling
    • alignment.compare_with() -- compare two alignments
    • alignment.append_model() -- copy model sequence and coordinates to alignment
    • 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.expand() -- put all models into alignment
    • alignment.segment_matching() -- align segments
  • 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
  • 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.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 info object: obtaining information about the MODELLER build
    • info.version -- return the full MODELLER version number
    • info.version_info -- return the version number, as a tuple
    • info.build_date -- return the date this binary was built
    • info.exe_type -- return the executable type of this binary
    • info.debug -- returns this binary's debug flag
    • info.time_mark() -- print current date, time, and CPU time
  • The log object: controlling the amount of output
    • log.level() -- Set all log output levels
    • 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
  
  
• 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
  
  
• 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
  
  
• Bibliography
• Index