phenix.pdbtools: PDB model manipulations and statistics


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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

Atomic Displacement parameters (ADP) statistics:

% phenix.pdbtools model.pdb --show-adp-statistics

Geometry (stereochemistry) statistics:

% phenix.pdbtools model.pdb --show-geometry-statistics

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). Structure factors calculation The total model structure factor is defined as:

Fmodel = scale * exp(-h*b_cart*ht) * (Fcalc + k_sol * exp(-b_sol*s^2) * Fmask)

where: scale is overall scale factor, h is Miller index, b_cart is overall anisotropic scale matrix in Cartesian basis, Fcalc are structure factors computed from atomic model, k_sol is bulk solvent density, b_sol is smearing factor for bulk solvent contribution, Fmask is a solvent mask. Add hydrogen atoms Add H atoms to a model using phenix.reduce. All default parameters of phenix.reduce are used. Perform model geometry regularization Minimize geometry target to idealize bond lenghths, bond angles, planarities, chiralities, dihedrals, and non-bonded interactions. 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) Simple Fcalc from atomic model (Fmodel = Fcalc):

% phenix.pdbtools model.pdb --f_model high_resolution=2.0

this will result in MTZ file with complete set of Fcalc up to 2A resolution. 7) Compute Fmodel include bulk solvent and all other scales, request the output in CNS format, specify labels for output Fmodel (by default it is FMODEL), set low_resolution limit, use direct method of calculations (rather than FFT):

% phenix.pdbtools model.pdb high_resolution=2.0 format=cns label=FM \
  low_resolution=6.0 algorithm=direct k_sol=0.35 b_sol=60 scale=3 \
  b_cart='1 2 -3 0 0 0' --f_model

8) Compute Fcalc using neutron scattering dictionary:

% phenix.pdbtools model.pdb --f_model high_resolution=2.0 scattering_table=neutron

9) Input model can be manipulated first before structure factors calculation:

% phenix.pdbtools model.pdb --f_model high_resolution=2.0 sites.shake=1.0

10) Add H atoms to a model:

% phenix.pdbtools model.pdb --add_h output.file_name=model_h.pdb

11) Model geometry regularization:

% phenix.pdbtools model.pdb --geometry_regularization

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
------------------------------------------------------------------------------- 
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
   random_seed= None Random seed
   adp Scope of options to modify ADP of selected atoms
      atom_selection= None Selection for atoms to be modified. Overrides
                      parent-level selection.
      randomize= None Randomize ADP within a certain range
      set_b_iso= None Set ADP of atoms to set_b_iso
      convert_to_isotropic= None Convert atoms to isotropic
      convert_to_anisotropic= None 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
      translate= 0 0 0 Translational shift
      rotate= 0 0 0 Rotational shift
      euler_angle_convention= *xyz zyz Euler angles convention to be used for
                              rotation
   occupancies Scope of options to modify occupancies of selected atoms
      randomize= None Randomize occupancies within a certain range
      set= None Set all or selected occupancies to given value
   output Write out PDB 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 .
input
   pdb
      file_name= None Model file(s) name (PDB)
   crystal_symmetry Unit cell and space group parameters
      unit_cell= None
      space_group= None
f_model
   high_resolution= None
   low_resolution= None
   r_free_flags_fraction= None
   k_sol= 0.0 Bulk solvent k_sol values
   b_sol= 0.0 Bulk solvent b_sol values
   b_cart= 0 0 0 0 0 0 Anisotropic scale matrix
   scale= 1.0 Overall scale factor
   scattering_table= wk1995 it1992 *n_gaussian neutron Choices of scattering
                     table for structure factors calculations
   structure_factors_accuracy
      algorithm= *fft direct
      cos_sin_table= False
      grid_resolution_factor= 1/3.
      quality_factor= None
      u_base= None
      b_base= None
      wing_cutoff= None
      exp_table_one_over_step_size= None
   mask
      solvent_radius= 1.11
      shrink_truncation_radius= 0.9
      grid_step_factor= 4.0 The grid step for the mask calculation is
                        determined as highest_resolution divided by
                        grid_step_factor. This is considered as suggested
                        value and may be adjusted internally based on the
                        resolution.
      verbose= 1
      mean_shift_for_mask_update= 0.1 Value of overall model shift in
                                  refinement to updates the mask.
      ignore_zero_occupancy_atoms= True Include atoms with zero occupancy into
                                   mask calculation
      ignore_hydrogens= True Ignore H or D atoms in mask calculation
   hkl_output
      format= *mtz cns
      label= FMODEL
      type= real *complex
      file_name= None Default is the original PDB file name with the file
                 extension replaced by .pdbtools.mtz or .pdbtools.cns
pdb_interpretation
   link_distance_cutoff= 3
   disulfide_distance_cutoff= 3
   chir_volume_esd= 0.2
   nonbonded_distance_cutoff= None
   default_vdw_distance= 1
   min_vdw_distance= 1
   nonbonded_buffer= 1
   vdw_1_4_factor= 0.8
   translate_cns_dna_rna_residue_names= None
   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
      cis_threshold= 45
      discard_psi_phi= True
      omega_esd_override_value= None
   rna_sugar_pucker_analysis
      use= True
      bond_min_distance= 1.2
      bond_max_distance= 1.8
      epsilon_range_not_2p_min= 155
      epsilon_range_not_2p_max= 310
      delta_range_2p_min= 115
      delta_range_2p_max= 180
      p_distance_c1_n_line_2p_max= 2.9
   show_histogram_slots
      bond_lengths= 5
      nonbonded_interaction_distances= 5
      dihedral_angle_deviations_from_ideal= 5
   show_max_lines
      bond_restraints_sorted_by_residual= 5
      nonbonded_interactions_sorted_by_model_distance= 5
      dihedral_angle_restraints_sorted_by_residual= 3
   clash_guard
      nonbonded_distance_threshold= 0.5
      max_number_of_distances_below_threshold= 100
      max_fraction_of_distances_below_threshold= 0.1
geometry_minimization
   alternate_nonbonded_off_on= False
   max_iterations= 500
   macro_cycles= 1
   show_geometry_restraints= False