Manipulations on a model in a PDB file including

The operations below can be applied to the whole model or selected parts (e.g. "selection=chain A and backbone"). See examples below.

• shaking of coordinates (random coordinate shifts)
• rotation-translation shift of coordinates
• shaking of occupancies
• set occupancies to a value
• shaking of ADP (B-factors)
• shifting of ADP (addition of a constant value)
• scaling of ADP (multiplication by a constant value)
• setting ADP to a given value
• conversion to isotropic or anisotropic ADP
• removal of selected parts of a model
• renumbering of residues
• truncation to poly-ALA
• convert SeMet residues to Met
• adjust segid field in PDB format

Graphical interface

As input, only a PDB file and appropriate geometry restraints (in CIF format are required. (The geometry restraints are actually optional if you uncheck the box "Stop for unknown residues", but they are strongly recommended.) Crystal symmetry is not essential but also recommended, and will be propagated to the output model.

Many different options are possible, only some of which are shown in the main window. The atom selection controls can be used to specify which part of the model will be affected by various changes, or to eliminate parts of the model. The operations on coordinates, B-factors, and occupancies also have separate (optional) atom selections.

(Note: in past versions PDBTools was also responsible for geometry minimization and addition of hydrogen atoms using Reduce; these methods have been moved to the programs phenix.geometry_minimization and phenix.ready_set, respectively.)

Command-line use

In the absence of a CRYST1 record in the PDB file, functionality that doesn't require knowledge of the crystal symmetry is still available. To enable the full functionality, the crystal symmetry can be specified externally (e.g. via the --symmetry option).

Some specific examples:

1) Type phenix.pdbtools from the command line for instructions:

% phenix.pdbtools

2) To see all default parameters:

% phenix.pdbtools --show-defaults=all

3) Suppose a PDB model consist of three chains A, B and C and some water molecules. Remove all atoms in chain C and all waters:

% phenix.pdbtools model.pdb remove="chain C or water"

or one can achieve exactly the same result with equivalent command:

% phenix.pdbtools model.pdb keep="chain A or chain B"

or:

% phenix.pdbtools model.pdb keep="not(chain C or water)"

or finally:

% phenix.pdbtools model.pdb remove="not(chain A or chain B)"

The result of all four equivalent commands above will be a new PDB file containing chains A and B only. Important: the commands keep and remove cannot be used simultaneously.

4) Remove all but backbone atoms and set all b-factors to 25:

% phenix.pdbtools model.pdb keep=backbone set_b_iso=25

5) Suppose a PDB model consist of three chains A, B and C and some water molecules. Remove all but backbone atoms and set b-factors to 25 for chain C atoms:

% phenix.pdbtools model.pdb keep=backbone set_b_iso=25 selection="chain C"

6) Show cmprehensive model statistics:

% phenix.pdbtools model.pdb model_statistics=true

List of all available keywords

• use_neutron_distances = False Use neutron X-H distances (which are longer than X-ray ones)
• model_statistics = None
• stop_for_unknowns = True
• job_title = None Job title in PHENIX GUI, not used on command line
• modify
  • remove = None Selection for the atoms to be removed
  • keep = None Select atoms to keep
  • put_into_box_with_buffer = None Move molecule into center of box.
  • selection = None Selection for atoms to be modified
  • change_of_basis = None Apply change-of-basis operator (e.g. reindexing operator) to the coordinates and symmetry. Example: a,c,b .
  • renumber_residues = False Re-number residues
  • increment_resseq = None Increment residue number
  • truncate_to_polyala = False Truncate a model to poly-Ala.
  • remove_alt_confs = False Deletes atoms whose altloc identifier is not blank or A , and resets the occupancies of the remaining atoms to 1.0.
  • always_keep_one_conformer = False Modifies behavior of remove_alt_confs so that residues with no conformer labeled blank or A are not deleted. Silent if remove_alt_confs is False.
  • set_chemical_element_simple_if_necessary = None Make a simple guess about what the chemical element is (based on atom name and the way how it is formatted) and write it into output file.
  • set_seg_id_to_chain_id = False Sets the segID field to the chain ID (padded with spaces).
  • clear_seg_id = False Erases the segID field.
  • convert_semet_to_met = False
  • remove_first_n_atoms_fraction = None
  • random_seed = None Random seed
  • move_waters_last = False Transfer waters to the end of the model. Addresses some limitations of water picking in phenix.refine.
  • adpScope of options to modify ADP of selected atoms
    • atom_selection = None Selection for atoms to be modified. Overrides parent-level selection.
    • randomize = False Randomize ADP within a certain range
    • set_b_iso = None Set ADP of atoms to set_b_iso
    • convert_to_isotropic = False Convert atoms to isotropic
    • convert_to_anisotropic = False Convert atoms to anisotropic
    • shift_b_iso = None Add shift_b_iso value to ADP
    • scale_adp = None Multiply ADP by scale_adp
  • sitesScope of options to modify coordinates of selected atoms
    • atom_selection = None Selection for atoms to be modified. Overrides parent-level selection.
    • shake = None Randomize coordinates with mean error value equal to shake
    • switch_rotamers = max_distant min_distant exact_match fix_outliers
    • translate = 0 0 0 Translational shift (x,y,z)
    • rotate = 0 0 0 Rotational shift (x,y,z)
    • euler_angle_convention = *xyz zyz Euler angles convention to be used for rotation
  • occupanciesScope of options to modify occupancies of selected atoms
    • atom_selection = None Selection for atoms to be modified. Overrides parent-level selection.
    • randomize = False Randomize occupancies within a certain range
    • set = None Set all or selected occupancies to given value
    • normalize = False Reset the sum of occupancies for each residue to 1.0. Note that this will be performed before any atoms are removed.
  • rotate_about_axis
    • axis = None
    • angle = None
    • atom_selection = None
  • rename_chain_idRename chains
    • old_id = None
    • new_id = None
  • set_charge
    • charge_selection = None
    • charge = None
  • outputWrite out file with modified model (file name is defined in write_modified)
    • file_name = None Default is the original file name with the file extension replaced by _modified.pdb .
    • format = *pdb mmcif Choose the output format of coordinate file (PDB or mmCIF)
• input
  • pdb
    • file_name = None Model file(s) name (PDB)
  • monomer_library
    • file_name = None Monomer file(s) name (CIF)
  • crystal_symmetryUnit cell and space group parameters
    • unit_cell = None
    • space_group = None
• pdb_interpretation
  • rdl = False
  • rotamer_data_version = *500 8000
  • cdl = False Use Conformation Dependent Library (CDL) for geometry minimization restraints
  • cdl_weight = 1.
  • correct_hydrogens = True
  • c_beta_restraints = True
  • use_neutron_distances = False Use neutron X-H distances (which are longer than X-ray ones)
  • disulfide_bond_exclusions_selection_string = None
  • exclusion_distance_cutoff = 3 If SG of CYS forming SS bond is closer than this distance to an atom that it may coordinate then this SG is excluded from SS bond.
  • link_distance_cutoff = 3
  • disulfide_distance_cutoff = 3
  • add_angle_and_dihedral_restraints_for_disulfides = True
  • peptide_nucleotide_distance_cutoff = 3
  • dihedral_function_type = *determined_by_sign_of_periodicity all_sinusoidal all_harmonic
  • chir_volume_esd = 0.2
  • max_reasonable_bond_distance = 50.0
  • nonbonded_distance_cutoff = None
  • default_vdw_distance = 1
  • min_vdw_distance = 1
  • nonbonded_buffer = 1 **EXPERIMENTAL, developers only**
  • nonbonded_weight = None Weighting of nonbonded restraints term. By default, this will be set to 16 if explicit hydrogens are used (this was the defaault in earlier versions of Phenix), or 100 if hydrogens are missing.
  • const_shrink_donor_acceptor = 0.6 **EXPERIMENTAL, developers only**
  • vdw_1_4_factor = 0.8
  • min_distance_sym_equiv = 0.5
  • custom_nonbonded_symmetry_exclusions = None
  • translate_cns_dna_rna_residue_names = None
  • proceed_with_excessive_length_bonds = False
  • automatic_linking
    • link_all = False If True, bond restraints will be generated for any appropriate ligand-protein or ligand-nucleic acid covalent bonds. This includes sugars, amino acid modifications, and other prosthetic groups.
    • link_metals = False
    • link_residues = False
    • link_carbohydrates = True
    • metal_coordination_cutoff = 3.5
    • amino_acid_bond_cutoff = 1.9
    • inter_residue_bond_cutoff = 2.2
    • buffer_for_second_row_elements = 0.5
    • carbohydrate_bond_cutoff = 1.99
  • resolution_dependent_restraints
    • load = False
    • resolution = Auto
    • resolution_range = high *med low
    • high_resolution_range_limit = 1.5
    • low_resolution_range_limit = 3.0
  • apply_cif_modification
    • data_mod = None
    • residue_selection = None
  • apply_cif_link
    • data_link = None
    • residue_selection_1 = None
    • residue_selection_2 = None
  • peptide_link
    • ramachandran_restraints = False Restrains peptide backbone to fall within allowed regions of Ramachandran plot. Although it does not eliminate outliers, it can significantly improve the percent favored and percent outliers at low resolution. Probably not useful (and maybe even harmful) at resolutions much higher than 3.5A.
    • cis_threshold = 45
    • discard_omega = False
    • discard_psi_phi = True
    • omega_esd_override_value = None
    • rama_weight = 1.0
    • scale_allowed = 1.0
    • rama_potential = *oldfield emsley
    • rama_selection = None
    • rama_exclude_sec_str = False
    • oldfield
      • esd = 10.0
      • weight_scale = 1.0
      • dist_weight_max = 10.0
      • weight = None
  • nucleic_acid_restraints
    • enabled = False If true special set of restraints for DNA/RNA nucleobases will be generated. This includes hydrogen bonds for basepairing interactions, planarity for basepairs and parallelity restraints for simulate stacking interactions.
    • save_as_param_file = False
    • bonds
      • enabled = True
      • restrain_angles = False
      • find_automatically = True
      • bond_distance_cutoff = 3.4
      • target_value = 2.89
      • sigma = 0.08
      • slack = 0.00
      • angle_between_bond_and_nucleobase_cutoff = 35.0 If angle between supposed hydrogen bond and basepair plane (defined by C4, C5, C6 atoms) is less than this value (in degrees), the bond will not be established.
    • basepair_planarity
      • enabled = True
      • find_automatically = True
      • sigma = 0.176
    • basepair_parallelity
      • enabled = False
      • find_automatically = True
      • target_angle_deg = 0
      • sigma = 0.027
      • slack = 0
      • top_out = False
      • limit = 1
    • stacking
      • enabled = True
      • find_automatically = True
      • sigma = 0.027
      • target_angle_deg = 0
      • slack = 0
      • top_out = False
      • limit = 1
      • skip_spatial_verification = False During this verification spatial organization is verified as described in Gendron et. al. (2001). JMB, 308, p. 919-936.
    • base_pairHere user should define by phenix selections at least one atom in each residue. One of the convinient ways to do so is to use resid 15 to define 15th residue.
      • base1 = None
      • base2 = None
    • stacking_pairHere user should define by phenix selections at least one atom in each residue. One of the convinient ways to do so is to use resid 15 to define 15th residue.
      • base1 = None
      • base2 = None
  • rna_sugar_pucker_analysis
    • bond_min_distance = 1.2
    • bond_max_distance = 1.8
    • epsilon_range_min = 155.0
    • epsilon_range_max = 310.0
    • delta_range_2p_min = 129.0
    • delta_range_2p_max = 162.0
    • delta_range_3p_min = 65.0
    • delta_range_3p_max = 104.0
    • p_distance_c1p_outbound_line_2p_max = 2.9
    • o3p_distance_c1p_outbound_line_2p_max = 2.4
    • bond_detection_distance_tolerance = 0.5
  • show_histogram_slots
    • bond_lengths = 5
    • nonbonded_interaction_distances = 5
    • bond_angle_deviations_from_ideal = 5
    • dihedral_angle_deviations_from_ideal = 5
    • chiral_volume_deviations_from_ideal = 5
  • show_max_items
    • not_linked = 5
    • bond_restraints_sorted_by_residual = 5
    • nonbonded_interactions_sorted_by_model_distance = 5
    • bond_angle_restraints_sorted_by_residual = 5
    • dihedral_angle_restraints_sorted_by_residual = 3
    • chirality_restraints_sorted_by_residual = 3
    • planarity_restraints_sorted_by_residual = 3
    • residues_with_excluded_nonbonded_symmetry_interactions = 12
    • fatal_problem_max_lines = 10
  • clash_guard
    • nonbonded_distance_threshold = 0.5
    • max_number_of_distances_below_threshold = 100
    • max_fraction_of_distances_below_threshold = 0.1
• geometry_restraints
  • edits
    • excessive_bond_distance_limit = 10
    • bond
      • action = *add delete change
      • atom_selection_1 = None
      • atom_selection_2 = None
      • symmetry_operation = None The bond is between atom_1 and symmetry_operation * atom_2, with atom_1 and atom_2 given in fractional coordinates. Example: symmetry_operation = -x-1,-y,z
      • distance_ideal = None
      • sigma = None
      • slack = None
    • angle
      • action = *add delete change
      • atom_selection_1 = None
      • atom_selection_2 = None
      • atom_selection_3 = None
      • angle_ideal = None
      • sigma = None
    • planarity
      • action = *add delete change
      • atom_selection = None
      • sigma = None
    • parallelity
      • action = *add delete change
      • atom_selection_1 = None
      • atom_selection_2 = None
      • sigma = 0.027
      • target_angle_deg = 0
    • scale_restraintsApply a scale factor to restraints for specific atom selections, to tighten geometry without changing the overall scale of the geometry target.
      • atom_selection = None
      • scale = 1.0
      • apply_to = *bond *angle *dihedral *chirality
  • remove
    • angles = None
    • dihedrals = None
    • chiralities = None
    • planarities = None
    • parallelities = None