phenix.secondary_structure_restraints

Description

It is a tool to generate secondary structure annotation in various formats using pdb file. When HELIX/SHEET records are present in input pdb file, no searching occurs, they are used as source of information about protein secondary structure. To force automatic detection of protein secondary structure elements, one needs to remove them from input file.

There are several methods available to search protein secondary structure:

ksdssp (default): uses KSDSSP
dssp: slightly different method by Nat Echols, stand-alone tool is mmtbx.dssp
from_ca: tries to find protein secondary structure from position of C-alpha atoms. Finds more SS elements than other methods, works better when the structure is distorted. (author Tom Terwilliger).
cablam: CaBLAM uses CA-trace geometry to validate protein backbone. Since the CA trace is more reliably modeled from low-resolution density than the full backbone trace, CaBLAM can identify modeling errors and intended secondary structure elements in low-resolution models. (author Christopher Williams).

Output format:

phenix (default): Phil parameter file suitable to use with all Phenix tools except phenix.refine
phenix.refine: Phil parameter file suitable to use with phenix.refine
pdb: HELIX/SHEET records in PDB format
pymol: output pymol script which can be loaded in pymol. It will display model with hydrogen bonds:

../images/ss_restraints_pymol_format.png

Command line usage examples

% phenix.secondary_structure_restraints model.pdb

% phenix.secondary_structure_restraints model.pdb format=phenix.refine

% phenix.secondary_structure_restraints model.pdb ignore_annotation_in_file=True

% phenix.secondary_structure_restraints model.pdb search_method=from_ca format=pdb

GUI

Graphical user interface is currently available under phenix.refine GUI, "Refinement settings" tab, select "Use secondary structure restraints" checkbox and click "Select Atoms" button.

List of all available keywords

show_all_params = False
filter_outliers = True
format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage csv
quiet = False
verbose = -1
output_prefix = None
ignore_annotation_in_file = False ignore annotation that is present in input file
file_name = None
secondary_structure
- ss_by_chain = True Find secondary structure only within individual chains. Alternative is to allow H-bonds between chains. Can be much slower with ss_by_chain=False. If your model is complete use ss_by_chain=True. If your model is many fragments, use ss_by_chain=False.
- from_ca_conservative = False various parameters changed to make from_ca method more conservative, hopefully to closer resemble ksdssp.
- max_rmsd = 1 Maximum rmsd to consider two chains with identical sequences as the same for ss identification
- use_representative_chains = True Use a representative of all chains with the same sequence. Alternative is to examine each chain individually. Can be much slower with use_representative_of_chain=False if there are many symmetry copies. Ignored unless ss_by_chain is True.
- max_representative_chains = 100 Maximum number of representative chains
- enabled = False Turn on secondary structure restraints (main switch)
- protein
  - enabled = True Turn on secondary structure restraints for protein
  - search_method = *ksdssp mmtbx_dssp from_ca cablam Particular method to search protein secondary structure.
  - distance_ideal_n_o = 2.9 Target length for N-O hydrogen bond
  - distance_cut_n_o = 3.5 Hydrogen bond with length exceeding this value will not be established
  - remove_outliers = True If true, h-bonds exceeding distance_cut_n_o length will not be established
  - restrain_hbond_angles = True
  - helix
    - serial_number = None
    - helix_identifier = None
    - enabled = True Restrain this particular helix
    - selection = None
    - helix_type = *alpha pi 3_10 unknown Type of helix, defaults to alpha. Only alpha, pi, and 3_10 helices are used for hydrogen-bond restraints.
    - sigma = 0.05
    - slack = 0
    - top_out = False
    - angle_sigma_scale = 1 Multiply sigmas for h-bond angles by this value. Original sigmas range from 5 to 10.
    - angle_sigma_set = None Use this parameter to set sigmas for h-bond angles to a particular value
    - hbond
      - donor = None
      - acceptor = None
  - sheet
    - enabled = True Restrain this particular sheet
    - first_strand = None
    - sheet_id = None
    - sigma = 0.05
    - slack = 0
    - top_out = False
    - angle_sigma_scale = 1 Multiply sigmas for h-bond angles by this value. Original sigmas range from 5 to 10.
    - angle_sigma_set = None Use this parameter to set sigmas for h-bond angles to a particular value
    - strand
      - selection = None
      - sense = parallel antiparallel *unknown
      - bond_start_current = None
      - bond_start_previous = None
    - hbond
      - donor = None
      - acceptor = None
- nucleic_acid
  - enabled = True Turn on secondary structure restraints for nucleic acids
  - hbond_distance_cutoff = 3.4 Hydrogen bonds with length exceeding this limit will not be established
  - angle_between_bond_and_nucleobase_cutoff = 35.0 If angle between supposed hydrogen bond and basepair plane (defined by C4, C5, C6 atoms) is less than this value (in degrees), the bond will not be established.
  - scale_bonds_sigma = 1. All sigmas for h-bond length will be multiplied by this number. The smaller number is tighter restraints.
  - base_pair
    - enabled = True Restraint this particular base-pair
    - base1 = None Selection string selecting at least one atom in the desired residue
    - base2 = None Selection string selecting at least one atom in the desired residue
    - saenger_class = 0 Type of base-pairing
    - restrain_planarity = False Apply planarity restraint to this base-pair
    - planarity_sigma = 0.176
    - restrain_hbonds = True Restrain hydrogen bonds length for this base-pair
    - restrain_hb_angles = True Restrain angles around hydrogen bonds for this base-pair
    - restrain_parallelity = True Apply parallelity restraint to this base-pair
    - parallelity_target = 0
    - parallelity_sigma = 0.0335
  - stacking_pair
    - enabled = True Restraint this particular base-pair
    - base1 = None Selection string selecting at least one atom in the desired residue
    - base2 = None Selection string selecting at least one atom in the desired residue
    - angle = 0
    - sigma = 0.027