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
• dynamics_type = *cartesian
• stop_at_diff = None stop after reaching specified cutoff value
• pdb_interpretation
  • rotamer_data_version = 500 *8000
  • 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
  • find_ncs = False
  • restraints_library
    • cdl = True Use Conformation Dependent Library (CDL) for geometry minimization restraints
    • omega_cdl = False Use Omega Conformation Dependent Library (omega-CDL) for geometry minimization restraints
    • rdl = False
  • secondary_structure
    • enabled = False
    • find_automatically = True
    • use_ksdssp = True Use KSDSSP program to annotate secondary structure. If False, a built-in DSSP method will be used instead.
    • helices_from_phi_psi = False
    • protein
      • enabled = 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
      • remove_outliers = True
      • substitute_n_for_h = None
      • 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
      • hbond_distance_cutoff = 3.4
      • 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
        • base1 = None
        • base2 = None
        • saenger_class = 0 reference
        • restrain_planarity = False
        • planarity_sigma = 0.176
        • restrain_hbonds = True
        • restrain_hb_angles = True
        • restrain_parallelity = True
        • parallelity_target = 0
        • parallelity_sigma = 0.0335
      • stacking_pair
        • base1 = None
        • base2 = None
        • enabled = True
        • angle = 0
        • sigma = 0.027
  • reference_coordinate_restraintsRestrains coordinates in Cartesian space to stay near their starting positions. This is intended for use in generating simulated annealing omit maps, to prevent refined atoms from collapsing in on the region missing atoms. For conserving geometry quality at low resolution, the more flexible reference model restraints should be used instead.
    • enabled = False
    • exclude_outliers = True
    • selection = all
    • sigma = 0.2
    • limit = 1.0
    • top_out = 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_none = False
    • link_metals = False
    • link_residues = False
    • link_amino_acid_rna_dna = False
    • link_carbohydrates = True
    • link_ligands = 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
    • ligand_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
  • 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
  • simple_ncs_from_pdb
    • pdb_in = None Input PDB file to be used to identify ncs
    • temp_dir = "" temporary directory (ncs_domain_pdb will be written there)
    • min_percent = 85. Threshold for similarity between chains, where similarity define as: (number of matching res) / (number of res in longer chain)
    • max_rmsd = 2. limit of rms difference between chains to be considered as copies
    • max_rmsd_user = None When given, overrides the max_rmsd
    • ncs_domain_pdb_stem = None NCS domains will be written to ncs_domain_pdb_stem+"group_"+nn
    • write_ncs_domain_pdb = False You can write out PDB files representing NCS domains for density modification if you want
    • verbose = False Verbose output
    • show_ncs_phil = True Show phil parameters for the NCS groups
    • show_summary = False Show NCS information summary
    • raise_sorry = False Raise sorry if problems
    • debug = False Debugging output
    • dry_run = False Just read in and check parameter names
    • ncs_file_format = *restraints constraints control the .ncs file format restraints: "refinement.ncs.restraint_group" constraints: "refinement.ncs.constraint_group"
    • minimize_param = *chains transforms chains : minimize the number of NCS related chains in each NCS groups. transforms : minimize the number of NCS operations
    • exclude_misaligned_residues = True check and exclude individual residues alignment quality
    • check_atom_order = True check atom order in matching residues
    • domain_finding_parameters
      • match_radius = 4.0 max allow distance difference between pairs of matching atoms of two residues
      • similarity_threshold = 0.95 Threshold for similarity between matching chains. A smaller value cause more chains to be grouped together and can lower the number of common residues
      • min_contig_length = 10 segments < min_contig_length rejected
  • ncs_group
    • reference = None Residue selection string for the complete master NCS copy
    • selection = None Residue selection string for each NCS copy location in ASU
  • ncs
    • check_atom_order = True check atom order in matching residues
    • use_minimal_master_ncs = True Minimize number of chains in master ncs groups
    • exclude_misaligned_residues = True check and exclude individual residues alignment quality
    • allow_different_size_res = True keep matching residue with different number of atoms
    • process_similar_chains = True When True, process chains that are close in length without raising errors
    • quiet = True quiet output when processing files
  • 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
  • remove
    • angles = None
    • dihedrals = None
    • chiralities = None
    • planarities = None
    • parallelities = None
• 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