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 along with pdb file to show hydrogen bonds

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
• 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
  • 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
      • 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
      • 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.
    • 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