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phenix.pdbtools: PDB model manipulations and statistics

List of all pdbtools keywords

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
  • 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 ADP
  • conversion to anisotropic ADP
  • removal of selected parts of a model
Comprehensive model statistics % phenix.pdbtools model.pdb model_statistics=true 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). Add hydrogen atoms Add H atoms to a model using phenix.reduce. All default parameters of phenix.reduce are used. 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"
% 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) Add H atoms to a model:
% phenix.pdbtools model.pdb --add_h output.file_name=model_h.pdb

List of all pdbtools keywords

Legend: black bold - scope names
        black - parameter names
        red - parameter values
        blue - parameter help
        blue bold - scope help
        Parameter values:
          * means selected parameter (where multiple choices are available)
          False is No
          True is Yes
          None means not provided, not predefined, or left up to the program
          "%3d" is a Python style formatting descriptor
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
   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
   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.
   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.
   adp Scope 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
   sites Scope 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
      max_rotomer_distortion= None Switch to a rotomer maximally distant from
                              the current one
      min_rotomer_distortion= None Switch to a rotomer minimally distant from
                              the current one
      translate= 0 0 0 Translational shift
      rotate= 0 0 0 Rotational shift
      euler_angle_convention= *xyz zyz Euler angles convention to be used for
   occupancies Scope of options to modify occupancies of selected atoms
      randomize= False Randomize occupancies within a certain range
      set= None Set all or selected occupancies to given value
      axis= None
      angle= None
      atom_selection= None
   rename_chain_id Rename chains
      old_id= None
      new_id= None
      charge_selection= None
      charge= None
   output Write out file with modified model (file name is defined in
      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
      file_name= None Model file(s) name (PDB)
      file_name= None Monomer file(s) name (CIF)
   crystal_symmetry Unit cell and space group parameters
      unit_cell= None
      space_group= None
   cdl= False Use Conformation Dependent Library (CDL) for geometry
        minimization restraints
   correct_hydrogens= True
   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
   peptide_nucleotide_distance_cutoff= 3
   dihedral_function_type= *determined_by_sign_of_periodicity all_sinusoidal
   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
      weight= False
      bonds= True
      angles= True
      factor= 1
      sqrt= False
      min_occupancy= 0.5
      intra_chain= False If True, bond restraints will be generated for any
                   appropriate ligand-protein or ligand-nucleic acid covalent
                   bonds if the chain IDs are the same. This includes sugars,
                   amino acid modifications, and other prosthetic groups.
      amino_acid_bond_cutoff= 1.9
      rna_dna_bond_cutoff= 3.5
      intra_residue_bond_cutoff= 1.99
      data_mod= None
      residue_selection= None
      data_link= None
      residue_selection_1= None
      residue_selection_2= None
      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
         esd= 10.0
         weight_scale= 1.0
         dist_weight_max= 10.0
         weight= None
      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
      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
      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
      nonbonded_distance_threshold= 0.5
      max_number_of_distances_below_threshold= 100
      max_fraction_of_distances_below_threshold= 0.1
      excessive_bond_distance_limit= 10
         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
         action= *add delete change
         atom_selection_1= None
         atom_selection_2= None
         atom_selection_3= None
         angle_ideal= None
         sigma= None
         action= *add delete change
         atom_selection= None
         sigma= None
      scale_restraints Apply 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
      angles= None
      dihedrals= None
      chiralities= None
      planarities= None