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MODELLER A Program for
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Symmetry restraints
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Index
M
ODELLER
command reference
Subsections
Key for command descriptions
The
Environ
class: M
ODELLER
environment
Environ() — create a new M
ODELLER
environment
Environ.io — default input parameters
Environ.edat — default objective function parameters
Environ.libs — M
ODELLER
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
EnergyData
class: objective function parameters
EnergyData() — create a new set of objective function parameters
EnergyData.contact_shell — nonbond distance cutoff
EnergyData.update_dynamic — nonbond recalculation threshold
EnergyData.sphere_stdv — soft-sphere standard deviation
EnergyData.dynamic_sphere — calculate soft-sphere overlap restraints
EnergyData.dynamic_lennard — calculate Lennard-Jones restraints
EnergyData.dynamic_coulomb — calculate Coulomb restraints
EnergyData.dynamic_modeller — calculate non-bonded spline restraints
EnergyData.excl_local — exclude certain local pairs of atoms
EnergyData.radii_factor — scale atomic radii
EnergyData.lennard_jones_switch — Lennard-Jones switching parameters
EnergyData.coulomb_switch — Coulomb switching parameters
EnergyData.relative_dielectric — relative dielectric
EnergyData.covalent_cys — use disulfide bridges in residue distance
EnergyData.nonbonded_sel_atoms — control interaction with picked atoms
EnergyData.nlogn_use — select non-bond list generation algorithm
EnergyData.max_nlogn_grid_cells — maximum number of grid cells for NlogN nonbond pairs routine
EnergyData.energy_terms — user-defined global energy terms
The
IOData
class: coordinate file input parameters
IOData() — create a new input parameters object
IOData.hetatm — whether to read HETATM records
IOData.hydrogen — whether to read hydrogen atoms
IOData.water — whether to read water molecules
IOData.convert_modres — whether to convert modified residues
IOData.hybrid36 — whether to read PDB files conformant with hybrid-36
IOData.two_char_chain — whether to read PDB files with two-character chain IDs
IOData.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
ConjugateGradients() — optimize atoms given restraints, with CG
QuasiNewton() — optimize atoms with quasi-Newton minimization
MolecularDynamics() — optimize atoms given restraints, with MD
actions.WriteStructure() — write out the model coordinates
actions.Trace() — write out optimization energies,
etc
actions.CHARMMTrajectory() — 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
GroupRestraints
class: restraints on atom groups
GroupRestraints() — create a new set of group restraints
GroupRestraints.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 plus insertion code
Residue.intnum — PDB-style residue number
Residue.inscode — PDB-style residue insertion code
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 —
χ
1
dihedral angle
Residue.chi2 —
χ
2
dihedral angle
Residue.chi3 —
χ
3
dihedral angle
Residue.chi4 —
χ
4
dihedral angle
Residue.chi5 —
χ
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
SequenceDB
class: using sequence databases
SequenceDB() — create a new sequence database
SequenceDB.read() — read a database of sequences
SequenceDB.close() — close an open database
SequenceDB.write() — write a database of sequences
SequenceDB.convert() — convert a database to binary format
SequenceDB.search() — search for similar sequences
SequenceDB.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 M
ODELLER
build
info.version — the full M
ODELLER
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 — M
ODELLER
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 M
ODELLER
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
SGEPEJob() — create a job using all Sun GridEngine (SGE) worker processes
SGEQsubJob() — create a job which can be expanded with Sun GridEngine 'qsub'
Job.worker_startup_commands — Worker 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 workers for message-passing
Communicator.send_data() — send data
Communicator.get_data() — get data
Worker.run_cmd() — run a command on the worker
LocalWorker() — create a worker running on the local machine
SGEPEWorker() — create a worker running on a Sun GridEngine parallel environment worker node
SGEQsubWorker() — create a 'qsub' worker running on a Sun GridEngine node
SSHWorker() — create a worker on a remote host accessed via ssh
of model