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
restraints = None
restraints_directory = None
use_neutron_distances = False Use neutron X-H distances (which are longer than X-ray ones)
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
use_c_beta_deviation_restraints = True
dynamics_type = *cartesian
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
- cdl = False Use Conformation Dependent Library (CDL) for geometry minimization restraints
- rdl = False
- correct_hydrogens = True
- 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
- 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.
- nonbonded_clashscore = False
- 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 = True
  - metal_coordination_cutoff = 3.5
  - amino_acid_bond_cutoff = 1.9
  - rna_dna_bond_cutoff = 3.5
  - link_residues = True
  - inter_residue_bond_cutoff = 2.5
  - buffer_for_second_row_elements = 0.5
  - link_carbohydrates = True
  - carbohydrate_bond_cutoff = 1.99
- 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
- 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
  - 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
secondary_structure
- 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
  - 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