Alternatives and complementary programs

• Simulated annealing has some advantages due to the ability to simultaneously de-bias and optimize the model against the data, which prevents the structure from unfolding at high temperatures. The main disadvantage is the much longer runtime.
• phenix.pdbtools can be used to reset B-factors, or shake coordiantes without geometry restraints. The latter is redundant if dynamics is run, but setting the B-factors to suitably low starting values (approximately 10 for most resolutions) will help remove bias.
• Both of the above steps can also be run at the start of phenix.refine; click the "Modify start model" button in the GUI to access options.
• To perturb structures for use as molecular replacement models, there is a separate program providing an interface to the normal modes method in Phaser (also available in the GUI under "Model tools"). This does a better job conserving local structure.

List of all available keywords

• silent = False
• write_geo_file = True
• file_name = None
• show_states = False
• restraints = None
• restraints_directory = None
• output_file_name_prefix = None
• directory = None
• job_title = None Job title in PHENIX GUI, not used on command line
• fix_rotamer_outliers = True Remove outliers
• stop_for_unknowns = True
• secondary_structure_restraints = False
• dynamics_type = *cartesian
• stop_at_diff = None stop after reaching specified cutoff value
• reference_restraints
  • restrain_starting_coord_selection = None Atom selection string: restraint selected to starting position
  • coordinate_sigma = 0.5 sigma value for coordinates restrained to starting positions
• pdb_interpretation
  • rdl = False
  • rotamer_data_version = *500 8000
  • cdl = False Use Conformation Dependent Library (CDL) for geometry minimization restraints
  • cdl_weight = 1.
  • correct_hydrogens = True
  • c_beta_restraints = True
  • use_neutron_distances = False Use neutron X-H distances (which are longer than X-ray ones)
  • 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
  • add_angle_and_dihedral_restraints_for_disulfides = True
  • 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
  • automatic_linking
    • link_all = False If True, bond restraints will be generated for any appropriate ligand-protein or ligand-nucleic acid covalent bonds. This includes sugars, amino acid modifications, and other prosthetic groups.
    • link_metals = False
    • link_residues = False
    • link_carbohydrates = True
    • metal_coordination_cutoff = 3.5
    • amino_acid_bond_cutoff = 1.9
    • inter_residue_bond_cutoff = 2.2
    • buffer_for_second_row_elements = 0.5
    • carbohydrate_bond_cutoff = 1.99
  • resolution_dependent_restraints
    • load = False
    • resolution = Auto
    • resolution_range = high *med low
    • high_resolution_range_limit = 1.5
    • low_resolution_range_limit = 3.0
  • 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
  • nucleic_acid_restraints
    • enabled = False If true special set of restraints for DNA/RNA nucleobases will be generated. This includes hydrogen bonds for basepairing interactions, planarity for basepairs and parallelity restraints for simulate stacking interactions.
    • save_as_param_file = False
    • bonds
      • enabled = True
      • restrain_angles = False
      • find_automatically = True
      • bond_distance_cutoff = 3.4
      • target_value = 2.89
      • sigma = 0.08
      • slack = 0.00
      • 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.
    • basepair_planarity
      • enabled = True
      • find_automatically = True
      • sigma = 0.176
    • basepair_parallelity
      • enabled = False
      • find_automatically = True
      • target_angle_deg = 0
      • sigma = 0.027
      • slack = 0
      • top_out = False
      • limit = 1
    • stacking
      • enabled = True
      • find_automatically = True
      • sigma = 0.027
      • target_angle_deg = 0
      • slack = 0
      • top_out = False
      • limit = 1
      • skip_spatial_verification = False During this verification spatial organization is verified as described in Gendron et. al. (2001). JMB, 308, p. 919-936.
    • base_pairHere user should define by phenix selections at least one atom in each residue. One of the convinient ways to do so is to use resid 15 to define 15th residue.
      • base1 = None
      • base2 = None
    • stacking_pairHere user should define by phenix selections at least one atom in each residue. One of the convinient ways to do so is to use resid 15 to define 15th residue.
      • base1 = None
      • base2 = 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
    • parallelity
      • action = *add delete change
      • atom_selection_1 = None
      • atom_selection_2 = None
      • sigma = 0.027
      • target_angle_deg = 0
    • scale_restraintsApply 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
    • parallelities = None
• secondary_structure
  • idealization
    • enabled = False
    • restrain_torsion_angles = False
    • sigma_on_reference_non_ss = 1
    • sigma_on_reference_helix = 1
    • sigma_on_reference_sheet = 0.5
    • sigma_on_torsion_ss = 5
    • sigma_on_torsion_nonss = 5
    • sigma_on_ramachandran = 1
    • sigma_on_cbeta = 2.5
    • n_macro = 3
    • n_iter = 300
  • input
    • file_name = None
    • use_hydrogens = True
    • include_helices = True
    • include_sheets = True
    • find_automatically = None
    • helices_from_phi_psi = False
    • force_nucleic_acids = False This will ignore the automatic chain type detection and run the base pair detection using PROBE even if no nucleic acids are found. Useful for tRNAs which have a large number of modified bases.
    • use_ksdssp = True Use KSDSSP program to annotate secondary structure. If False, a built-in DSSP method will be used instead.
  • h_bond_restraints
    • verbose = False
    • substitute_n_for_h = None
    • restrain_helices = True
    • alpha_only = False
    • restrain_sheets = True
    • restrain_base_pairs = True
    • remove_outliers = True
    • distance_ideal_n_o = 2.9
    • distance_cut_n_o = 3.5
    • distance_ideal_h_o = 1.975
    • distance_cut_h_o = 2.5
    • sigma = 0.05
    • slack = 0.0
    • top_out = False
  • 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.
    • restraint_sigma = None
    • restraint_slack = None
    • backbone_only = False Only applies to rigid-body groupings, and not H-bond restraints which are already backbone-only.
  • sheet
    • first_strand = None
    • sheet_id = None
    • restraint_sigma = None
    • restraint_slack = None
    • 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
  • nucleic_acids
    • sigma = None Defaults to global setting
    • slack = None Defaults to global setting
    • use_db_values = True
    • base_pair
      • base1 = None
      • base2 = None
      • saenger_class = None reference
      • leontis_westhof_class = *Auto wwt reference
• cartesian_dynamics
  • temperature = 300
  • number_of_steps = 200
  • time_step = 0.0005
  • initial_velocities_zero_fraction = 0
  • n_print = 100
  • verbose = -1
  • random_seed = None
  • n_collect = 10
  • stop_cm_motion = True