phenix.dynamics: simple model perturbation

This program performs very crude molecular dynamics on a model, usually for the purpose of removing any bias in R-free due to previous refinement against a different test set. It is not suitable for generating physically realistic trajectories, due to the lack of attractive forces such as electrostatics, and lengthy runs will result in the model falling apart. However, it is very effective for de-biasing while maintaining approximately correct geometry, and is also very fast (unlike simulated annealing in phenix.refine).

The inputs for the program are very similar to those for phenix.geometry_minimization; the only required files are a model and any necessary restraints (CIF) files for non-standard ligands. By default the dynamics is run at approximately room temperature; higher temperatures will result in faster movement. Note however that unlike simulated annealing, the model will tend to unfold rapidly at high temperatures.

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
allow_allowed_rotamers = True More strict fixing outliers
stop_for_unknowns = True
dynamics_type = *cartesian
stop_at_diff = None stop after reaching specified cutoff value
pdb_interpretation
- sort_atoms = True
- superpose_ideal_ligand = *None all SF4 F3S
- flip_symmetric_amino_acids = False
- disable_uc_volume_vs_n_atoms_check = False
- 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
- 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 default 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
- 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
  - hpdl = False
- 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
- 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
- include_in_automatic_linking
  - selection_1 = None
  - selection_2 = None
  - bond_cutoff = 4.5
- exclude_from_automatic_linking
  - selection_1 = None
  - selection_2 = None
- apply_cis_trans_specification
  - cis_trans_mod = cis *trans
  - residue_selection = None Residues containing C-alpha atom of omega dihedral
- apply_cif_restraints
  - restraints_file_name = None
  - residue_selection = None
- 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
  - apply_all_trans = False
  - discard_omega = False
  - discard_psi_phi = True
  - apply_peptide_plane = False
  - 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
    - plot_cutoff = 0.027
- 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
- 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_search
  - enabled = False Use NCS restraints or constraints in refinement (can be determined automatically)
  - exclude_selection = "not (protein or nucleotide) or element H or element D" Atoms selected by this selection will be excluded from the model before search procedures will run.
  - chain_similarity_threshold = 0.85 Threshold for similarity between matching chains. A smaller value cause more chains to be grouped together and can lower the number of common residues
  - chain_max_rmsd = 2. limit of rms difference between chains to be considered as copies
  - residue_match_radius = 4.0 Max allowed distance difference between pairs of matching atoms of two residues
- 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
  - dihedral
    - action = *add delete change
    - atom_selection_1 = None
    - atom_selection_2 = None
    - atom_selection_3 = None
    - atom_selection_4 = None
    - angle_ideal = None
    - sigma = None
    - periodicity = 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
reference_model
- enabled = False Restrains the dihedral angles to a high-resolution reference structure to reduce overfitting at low resolution. You will need to specify a reference PDB file (in the input list in the main window) to use this option.
- file = None
- use_starting_model_as_reference = False
- sigma = 1.0
- limit = 15.0
- hydrogens = False
- main_chain = True
- side_chain = True
- fix_outliers = True
- strict_rotamer_matching = False
- auto_shutoff_for_ncs = False
- secondary_structure_only = False
- reference_group
  - reference = None
  - selection = None
  - file_name = None this is to used internally to disambiguate cases where multiple reference models contain the same chain ID. This normally does not need to be set by the user
- search_options
  - exclude_selection = "not (protein or nucleotide) or element H or element D" Atoms selected by this selection will be excluded from the model before search procedures will run.
  - chain_similarity_threshold = 0.85 Threshold for similarity between matching chains. A smaller value cause more chains to be grouped together and can lower the number of common residues
  - chain_max_rmsd = 100. limit of rms difference between chains to be considered as copies
  - residue_match_radius = 1000 Max allowed distance difference between pairs of matching atoms of two residues
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