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.
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) Add H atoms to a model:
% phenix.pdbtools model.pdb --add_h output.file_name=model_h.pdb
7) 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
-------------------------------------------------------------------------------
model_statistics= None
stop_for_unknowns= True
regularize_geometry= False
simple_dynamics= False Shake atoms while maintaining proper geometry. Not
intended to be physically realistic, but useful for testing
purposes.
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
renumber_residues= False Re-number residues
truncate_to_polyala= False Truncate a model to poly-Ala. If True, other
options will be ignored.
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. If True, other options will be ignored.
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.
remove_first_n_atoms_fraction= None
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= 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
rotation
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
rotate_about_axis
axis= None
angle= None
atom_selection= None
rename_chain_id Rename chains
old_id= None
new_id= None
set_charge
charge_selection= None
charge= None
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)
monomer_library
file_name= None Monomer file(s) name (CIF)
crystal_symmetry Unit cell and space group parameters
unit_cell= None
space_group= None
pdb_interpretation
cdl= False Use Conformation Dependent Library (CDL) for geometry
minimization restraints
correct_hydrogens= False
link_distance_cutoff= 3
disulfide_distance_cutoff= 3
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 when hydrogen
atoms are omitted. When explicit hydrogens are present,
the weight will be set to 16, which was the default in
previous versions.
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
altloc_weighting
weight= False
bonds= True
angles= True
factor= 1
sqrt= True
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
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
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
cartesian_dynamics
temperature= 300
number_of_steps= 200
time_step= 0.0005
initial_velocities_zero_fraction= 0
n_print= 100
verbose= -1
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