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"
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
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
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
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
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 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_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= 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
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
altloc_weighting
weight= False
bonds= True
angles= True
factor= 1
sqrt= False
min_occupancy= 0.5
automatic_linking
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
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
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
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
remove
angles= None
dihedrals= None
chiralities= None
planarities= None
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