Manipulations on a model in a PDB file including

The operations below can be applied to the whole model or selected parts (e.g. "modify.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

Video Tutorial

The tutorial video is available on the Phenix YouTube channel and covers the following topics:

• basic overview
• how to run PDBTools via the GUI
• example 1: prepare model file for usage with lower resolution data
• example 2: convert all residues in a model to alanine

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

Some specific examples:

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

% phenix.pdbtools

2) To see all default parameters:

% phenix.pdbtools

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 water and set all b-factors to 25:

% phenix.pdbtools model.pdb remove=water set_b_iso=25

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

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

List of all available keywords

• 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
  • flip_symmetric_amino_acids = False Flip symmetric amino acid side chains
  • 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.
  • truncate_to_polygly = False Truncate a model to poly-Gly.
  • 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
  • convert_met_to_semet = False
  • neutralize_scatterers = False
  • remove_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
  • 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