[main] ; ------------------------- Main parameters ---------------------------------- # ; Leave these fields empty in order to use default files ; ariaproject_template : For backward compatibility with different ; versions of ARIA since there is several ; differences between aria templates.This package ; can switch between 6 version actually: ; - 2.3.0 with ramachandran potential tag ; - 2.3.2 with exponent tag ; - 2.3.3 with clustering tag ; - 2.3.4 with scoring tag ; - 2.3.5 with avg_exponent field in ambiguous ; restraint tag ; - 2.3.6 with method field in clustering tag ss_dist_file: scsc_min_file: interlowerbounds_pdbstat: intertarget_pdbstat: interupperbounds_pdbstat: intralowerbounds_pdbstat: intratarget_pdbstat: intraupperbounds_pdbstat: ariaproject_template: 2.3.8 procheck_executable: prosa_executable: whatif_executable: clashlist_executable: [contactdef] ; Contact definition section used to define maplot from pdb file. ; Decrease this threshold if using other cutoff (e.g. 5.0) default_cutoff: 8.0 ; Add contact cutoff folowwing the syntax all, atm1_atm2 or sc_sc for side chains ;all: ;ca_ca: ;cb_cb: ;sc_sc: [setup] ; ------------------------------ TBL parameters ------------------------------ # ; longrange_hb : True, False [False] ; use long range hbond restraints. If there is ; no hbond map given, use the naive method from ; METAPSICOV (Take the top nf_longrange_hb * seq ; length predicted contacts from the contactlist ; and set those who are in a beta sheet as hb ; nf_longrange_hb : Float [0.1] ; Number hbond generated = nf * seq length ; longrange_hbtype : main, all [main] ; Consider short range hbond only as main chain ; hydrogen bond or for all donor/acceptor ; hb_dminus/dplus : Float [0.0, 0.5] ; distance bound in tbl restraints longrange_hb: False nf_longrange_hb: 0.1 longrange_hbtype: main hb_dminus: 0.0 hb_dplus: 0.5 ; ---------------------- Distance restraint parameters ----------------------- # ; native_reliable : True, False [False] ; Define native contact map as reliable in aria ; iterative protocol. Those contacts will not be ; filtered. ; evfold_weight : True, False [False] ; use EVFold weight -> 10/i (i:contact rank) for ; contact map derived distance restraints in ; aria protocol ; neighborhood_contact : True, False [False] ; Generate restraints for neighbors foreach ; contact in the contact map ; atom_groups : all, heavy, min [min] ; use all, heavy atms or from a minimized ; list (CA, CB, SC) for contribution list for ; each distance restraint ; contributions_type : same, allvsall, onevsall [same] ; By default contributions list will be a ; simple list between atoms of the same type ; (CA-CA, CB-CB, ...). Otherwise, compute ; pairwise product between contribution ; lists of the 2 residues (onevsall and ; allvsall). In the case of ADR, onevsall will ; generate one ADR for all contribution pairs ; between an atom of the first residue against ; all the other atoms in the second residue ; distance_type : fixed, pdbstat, distfile [fixed] ; Define distance use for target distance. By ; default the target distance is fixed by ; parameters listed below. Otherwise a distance ; map derived from pdb distance distribution ; (not yet implemented) or given by the user can ; be used. ; pdbdistance_level : ss, res, ; groupby_method : mean, min, deff [min] ; If a distance map is used for setting distance ; target, define if we use min, mean or deff ; distance on all the possible values. ; ambiguous_distance_restraint : True, False [False] ; Generate Ambiguous Distance Restraints. ; Otherwise, each distance restraints will have ; only one contribution (unambiguous distance ; restraints) native_reliable: False evfold_weight: False neighborhood_contact: False atom_groups: min contributions_type: same distance_type: fixed groupby_method: min deffpow: 6 pdbdistance_level: ss ambiguous_distance_restraint: False ; Parameters below used only when distance_type is set to "fixed" restraint_distance: 2.5 lower_bound: 1.0 def_upper_bound: 5.0 ; Specific tresholds only for unambig restraints ca_upper_bound: 7.0 cb_upper_bound: 7.0 ; ---------------------------- Filter parameters ----------------------------- # ; n_factor : float [1.0] ; Factor used for selection of contacts according to their score ; (n * n_factor with n as sequence length) ; contactfilter : all or combination of pos, cons, cys, ssclash separated by "+" ; character [pos] ; If empty, use only position filter (avoid short range ; restraints) n_factor: 1.0 contactfilter: all ; conservation_treshold : Float [95] ; Remove contact with highly conservated residues ; position_treshold : Int [5] ; Remove short range contacts conservation_treshold: 95 position_treshold: 5 ; seed : If no scoremap to select top n contacts, choose a subset wit ; random.sample method. For reproductibility, the seed used for ; the sampling is provided here seed: 89764443 ; net_deconv : use network deconvolution to filter contact map ; nd_beta : eigenvalue scaling parameter for network deconvolution. ; Corresponding to propagation of indirect effects over ; longer indirect paths. ; nd_alpha : Network density parameter corresponding to the use of the ; full mutual information and direct information matrices net_deconv: False nd_beta: 0.99 nd_alpha: 1.0 ; --------------------------- ARIA XML parameters ---------------------------- # runid: 1 cpus: 100 host_command: "sbatch -t 02:00:00" host_executable: temp_root: examples/tmp parameter_definition: automatic ss_dist_format: tbl ss_dist_enabled: yes ss_dist_add_to_network: no ss_dist_calibrate: no ss_dist_run_network_anchoring: no ss_dist_filter_contributions: no dist_format: xml dist_enabled: yes dist_add_to_network: no dist_calibrate: no dist_run_network_anchoring: no dist_filter_contributions: yes dist_avg_exponent: 6 cns_executable: cns_keep_output: no unambiguous_restraints_k_cool1_initial: 10.0 unambiguous_restraints_k_cool1_final: 50.0 unambiguous_restraints_k_cool2: 50.0 hbond_restraints_k_cool1_initial: 10.0 hbond_restraints_k_cool1_final: 50.0 hbond_restraints_k_cool2: 50.0 dihedral_restraints_k_cool1: 25.0 dihedral_restraints_k_cool2: 200.0 logharmonic_potential_enabled: no logharmonic_potential_use_auto_weight: no logharmonic_potential_weight_unambig: 25.0 logharmonic_potential_weight_ambig: 10.0 logharmonic_potential_weight_hbond: 25.0 rama_potential_enabled: yes hbdb_potential_enabled: no scoring_method: standard md_parameters_dynamics: torsion md_parameters_tad_temp_high: 10000.0 md_parameters_tad_timestep_factor: 9.0 md_parameters_cartesian_temp_high: 2000.0 md_parameters_cartesian_first_iteration: 0 md_parameters_timestep: 0.003 md_parameters_temp_cool1_final: 1000.0 md_parameters_temp_cool2_final: 50.0 md_parameters_steps_refine: 4000 md_parameters_random_seed: 89764443 md_parameters_steps_high: 10000 md_parameters_steps_cool1: 5000 md_parameters_steps_cool2: 4000 water_refinement_solvent: water water_refinement_n_structures: 10 water_refinement_enabled: yes water_refinement_write_solvent_molecules: no structures_analysis_enabled: yes procheck_executable: procheck_enabled: no prosa_executable: prosa_enabled: no whatif_executable: whatif_enabled: no clashlist_executable: clashlist_enabled: no pickle_output: no ; --------------------------- Iteration parameters --------------------------- # ; /!\ Parameters below can be formatted as a list if we want different values ; foreach iteration. Actually, only 2 parameters can be set with different ; values for each iterations (violation tolerance and partial assignment weight ; treshold) iterations: 8 iteration_n_structures: 100 iteration_sort_criterion: total_energy iteration_n_best_structures: 15 iteration_n_kept_structures: 0 merging_method: standard calib_relaxation_matrix: no calib_distance_cutoff: 6.0 calib_estimator: ratio_of_averages calib_error_estimator: distance viol_violation_tolerance: 1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1 viol_violation_threshold: 0.5 viol_sigma_mode: fix partassign_weight_threshold: 1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8 partassign_max_contributions: 1000 partassign_exponent: 6 netanch_high_residue_threshold: 4.0 netanch_enabled: no netanch_min_residue_threshold: 1.0 netanch_min_atom_threshold: 0.25 clustering_enabled: yes,yes,yes,yes,yes,yes,yes,yes,yes clustering_mask: CA clustering_nclusters: 2 clustering_method: kmeans [maplot] ; -------------------------- Contactmap parameters --------------------------- # ; Report settings ; n_factors: Number of EC tested: n * n_factor (n: sequence length) n_factors: 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0 ; Plot settings save_fig: True heatmap_linewidths: 0.0 size_fig: 10 plot_ext: pdf plot_dpi: 200 alpha: 1.0 [bbconv] ; -------------------------- bbconverter parameters -------------------------- # couplingmatrix: start: end: outputprefix: PSIPREDfile: diversityvalue: L: [pdbqual] trash_directory: /tmp skip_prefix: fitted csh_executable: csh [pdbdist] ; ----------------------- PDB distribution parameters ------------------------ # ; contact_cutoff: float [4.5] ; Cutoff used to search neighbor atoms ; dssp_exec: path ; Path of DSSP executable contact_cutoff: 4.5 dssp_exec: /c6/shared/bin/dssp download_pdbs: True obsolete_directory: /tmp/obsolete remove_pdbs: False pair_list: min [pdbstat] ; mode: simple [simple] ; Extract minimal distance, mean of minimal mode, maximal distance from ; distance distribution to define bounds in serialized dictionaries ; groups: {ss,res,atm} [ss+res+atm] ; Group levels in serialized dictionaries mode: simple groups: ss+atm+res sample_minsize: 20 [analysis] atmask: CA violation_treshold: 0.5 nbest_structures: 15 sort_criterion: total_energy