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.

If input .pdb file contains unknown ligands, their description should be supplied. This description can be obtained using eLBOW (GUI version)

The model should not contain non-standard protein residues inside secondary structure elements. The presence of unknown (UNK) residues in model (outside SS elements) is not advised because appropriate geometry restraints will not be generated for them and therefore such residues may be significantly distorted.

Command line usage examples

% phenix.model_idealization model.pdb

GUI

Not available

List of all available keywords

• model_file_name = None
• map_file_name = None User-provided map that will be used as reference
• hkl_file_name = None User-provided X-ray data to generate 2mFo-DFc map that will be used as reference
• data_labels = None Labels for experimental data.
• r_free_flags_labels = None Labels for free reflections.
• ligands_file_name = None User-provided ligand restraints
• mask_and_he_map = False Mask and histogram equalization of the input map
• trim_alternative_conformations = False Leave only atoms with empty altloc
• additionally_fix_rotamer_outliers = True At the late stage if rotamer is still outlier choose another one with minimal clash with surrounding atoms
• use_ss_restraints = True Use Secondary Structure restraints
• use_starting_model_for_final_gm = False Use supplied model for final geometry minimization. Otherwise just use self.
• output_prefix = None
• output_pkl = False
• output_model_h = True
• use_map_for_reference = True
• run_minimization_first = True
• run_minimization_last = True
• use_hydrogens_in_minimization = False
• reference_map_resolution = 5
• number_of_refinement_cycles = 5
• cycles_to_converge = 2 Nuber of cycles of geometry optimization without considerable stat change before stopping
• ignore_ncs = False Don't use NCS even if it is present in model.
• filter_input_ss = True Filter input annotation
• debug = False Output all intermediate files
• verbose = False More output to log
• nonbonded_weight = 10000
• apply_all_trans = True
• rama_weight = 1.0
• scale_allowed = 1.0
• rama_potential = *oldfield emsley
• rama_selection = None Selection of part of the model for which Ramachandran restraints will be set up.
• restrain_rama_outliers = True Apply restraints to Ramachandran outliers
• restrain_rama_allowed = True Apply restraints to residues in allowed region on Ramachandran plot
• restrain_allowed_outliers_with_emsley = False In case of restrain_rama_outliers=True and/or restrain_rama_allowed=True still restrain these residues with emsley. Make sense only in case of using oldfield potential.
• ss_idealization
  • enabled = True Enable secondary structure idealization
  • file_name_before_regularization = None
  • skip_empty_ss_elements = True skip SS element if there is no atoms in the structure
  • skip_good_ss_elements = False Skip SS elements without wrong/outlier Ramachandran angles and with reasonable hydrogen bonds length
  • restrain_torsion_angles = False Restrain torsion angles
  • fix_rotamer_outliers = True Fix rotamer outliers after replacing SS elements
  • 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 = Auto
  • n_iter = 300
  • nproc = 1
  • verbose = False
• oldfield
  • esd = 10.0
  • weight_scale = 1.0
  • dist_weight_max = 10.0
  • weight = None
  • plot_cutoff = 0.027
• 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
• loop_idealization
  • enabled = True
  • output_prefix = None
  • minimize_whole = True
  • fix_rotamers = True Fix rotamers before minimization
  • force_rama_fixes = False If true, the procedure will pick and apply the best variant even if all of them are above thresholds to be picked straight away. Alternatively, when False, the procedure will accept failure and leave a ramachandran outlier intact.
  • include_allowed = False Try to fix residues in allowed Ramachandran region with CCD
  • avoid_allowed_region = False If true, CCD will not let residues go to allowed region on Ramachandran plot
  • make_all_trans = True If true, procedure will try to get rid of all twisted and cis-peptides making all of them trans.
  • save_states = False Save states of CCD. Generates a states file for every model. Warning! Significantly slower!
  • number_of_ccd_trials = 3 How many times we are trying to fix outliers in the same chain
  • variant_search_level = 2 how thoroughly variants will be explored (1-3)
  • variant_number_cutoff = 50 how many first variants to take from generated
  • variant_deviation_accept_level = low *med high very_high what deviation from starting model is acceptable when screening variants. med is fine for real-space, low is for reciprocal space.
  • expert_level = 2
  • debug = False Output of intermediate files
• cablam_idealization
  • enabled = True
  • nproc = 1 Parallelization is not implemented
  • do_gm = False Run geometry minimization after rotation
  • find_ss_after_fixes = True re-evaluate SS after fixing Cablam outliers. May be helpful to identify new or extend previous SS elements
  • save_intermediates = False Save all cablam rotation for particular residue in separate file