Description

The program for geometry idealization of protein secondary structure.

Program reads model from .pdb file, extracts information from HELIX/SHEET records if available and replaces these helices and sheets with geometrically ideal ones while preserving initial atom positions as much as possible.

If HELIX/SHEET records are not available, it will try to find them automatically. Correct secondary structure annotation is extremely important for proper functioning of this program. Incorrect annotations most likely will lead to distorted model. Please refer to SS documentation for more details.

Command line usage examples

% phenix.model_idealization model.pdb

GUI

Not available

List of all available keywords

• file_name = None
• model_idealization
  • enabled = False Enable secondary structure idealization
  • file_name_before_regularization = None
  • restrain_torsion_angles = False Restrain torsion angles
  • sigma_on_reference_non_ss = 1 Weight on original model coordinates restraints where no ss present. Keeps loops close to initial model. (bigger number gives lighter restraints)
  • sigma_on_reference_helix = 1 Weight on original model coordinates restraints where helix present. Bends helices a bit according to initial model. (bigger number gives lighter restraints)
  • sigma_on_reference_sheet = 0.5 Weight on original model coordinates restraints where sheet present. Bends helices a bit according to initial model. (bigger number gives lighter restraints)
  • sigma_on_torsion_ss = 5 Weight on torsion angles restraints where ss present. Keeps helices torsion angles close to ideal. (bigger number gives lighter restraints)
  • sigma_on_torsion_nonss = 5
  • sigma_on_ramachandran = 1
  • sigma_on_cbeta = 2.5
  • n_macro = 3
  • n_iter = 300
• 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 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
    • 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
      • backbone_only = False Only applies to rigid-body groupings, and not H-bond restraints which are already backbone-only.
      • 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