Hi, I would like to do TLS but every time I try to start it I get following error: File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 69, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/driver.py", line 199, in __init__ value = 0.0) File "/usr/local/cci_apps-1421/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 735, in generate_tlsos origins.append(xrs.center_of_mass()) File "/usr/local/cci_apps-1421/cci_apps_sources/cctbx/cctbx/xray/structure.py", line 943, in center_of_mass return self.sites_cart().mean_weighted(weights=atomic_weights) RuntimeError: mean_weighted() argument is an empty array I've attached my input file. Any suggestions on what I'm doing wrong would be greatly appreciated. Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[@]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940 # Default parameters for subsequent refinement # Date 2008-05-16 Time 18:33:47 EEST +0300 (1210952027.81 s) # Command to extract only non-defaults: # phenix.refine --diff-params "h135d-mg_007.def" refinement { crystal_symmetry { unit_cell = 70.31999969 173.0200043 54.97000122 90 90 90 space_group = "P 21 21 2" } input { pdb { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/h135d-mg_006.pdb" } neutron_data { ignore_xn_free_r_mismatch = False file_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True sigma_fobs_rejection_criterion = 0 sigma_iobs_rejection_criterion = 0 ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None r_free_flags { file_name = None label = None test_flag_value = None disable_suitability_test = False ignore_pdb_hexdigest = False ignore_r_free_flags = False generate = False fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } } xray_data { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" labels = "I-obs,SIGI-obs" high_resolution = None low_resolution = None outliers_rejection = True sigma_fobs_rejection_criterion = 0 sigma_iobs_rejection_criterion = 0 ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None r_free_flags { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" label = "R-free-flags" test_flag_value = 1 disable_suitability_test = False ignore_pdb_hexdigest = False ignore_r_free_flags = False generate = False fraction = 0.05 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } } experimental_phases { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" labels = "HLA,HLB,HLC,HLD" } monomers { file_name = None } symmetry_safety_check = *error warning } output { prefix = "h135d-mg" serial = 7 serial_format = "%03d" write_eff_file = True write_geo_file = True write_def_file = True export_final_f_model = mtz cns write_maps = True write_map_coefficients = True } electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None } map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.3333333333 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False } refine { strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ occupancies group_anomalous sites { individual = None rigid_body = "chain A" rigid_body = "chain B" } adp { individual { isotropic = all anisotropic = None } group = None one_adp_group_per_residue = True tls = "(chain A and resid 030:060)" tls = "(chain A and resid 061:135)" tls = "(chain A and resid 136:165)" tls = "(chain A and resid 166:190)" tls = "(chain A and resid 191:244)" tls = "(chain A and resid 245:307)" tls = "(chain A and resid 308:328)" tls = "(chain A and resid 329:375)" tls = "(chain B and resid 030:060)" tls = "(chain B and resid 061:135)" tls = "(chain B and resid 136:165)" tls = "(chain B and resid 166:190)" tls = "(chain B and resid 191:244)" tls = "(chain B and resid 245:307)" tls = "(chain B and resid 308:328)" tls = "(chain B and resid 329:375)" } occupancies { individual = None group = None one_occupancy_group_per_residue = False } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime } } } main { bulk_solvent_and_scale = True simulated_annealing = False ordered_solvent = False ncs = False ias = False number_of_macro_cycles = 3 max_number_of_iterations = 12 use_form_factor_weights = False tan_u_iso = False use_convergence_test = False target = ml *mlhl ml_sad ls min_number_of_test_set_reflections_for_max_likelihood_target = 50 max_number_of_resolution_bins = 30 reference_xray_structure = None use_experimental_phases = None compute_optimal_errors = False random_seed = 3326496 scattering_table = wk1995 it1992 *n_gaussian neutron use_normalized_geometry_target = True target_weights_only = False use_f_model_scaled = False max_d_min = 0.25 fake_f_obs = False optimize_mask = False occupancy_max = 1 occupancy_min = 0.1 stir = None rigid_bond_test = False show_residual_map_peaks_and_holes = True fft_vs_direct = False outliers_rejection = True find_and_add_hydrogens = False } modify_start_model { selection = None adp { selection = None randomize = None set_b_iso = None convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } sites { selection = None shake = None translate = "0" "0" "0" rotate = "0" "0" "0" euler_angle_convention = *xyz zyz } occupancies { randomize = False set = None } output { file_name = None } random_seed = None } fake_f_obs { k_sol = 0 b_sol = 0 b_cart = "0" "0" "0" "0" "0" "0" scale = 1 structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True } scattering_table = wk1995 it1992 *n_gaussian neutron } hydrogens { refine_sites = individual *riding refine_adp = one_b_per_residue *one_b_per_molecule individual refine_occupancies = one_q_per_residue *one_q_per_molecule individual contribute_to_f_calc = True xh_bond_distance_deviation_limit = 0 build { map_type = "mFobs-DFmodel" map_cutoff = 2 angular_step = 3 use_sigma_scaled_maps = True resolution_factor = 0.25 map_next_to_model { min_model_peak_dist = 0.7 max_model_peak_dist = 1.05 min_peak_peak_dist = 1 use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1 } } } group_b_iso { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False } adp { iso { max_number_of_iterations = 25 automatic_randomization_if_all_equal = True scaling { scale_max = 3 scale_min = 10 } } } tls { one_residue_one_group = None refine_T = True refine_L = True refine_S = True number_of_macro_cycles = 2 max_number_of_iterations = 25 start_tls_value = None run_finite_differences_test = False eps = 1e-06 } adp_restraints { iso { use_u_local_only = False sphere_radius = 5 distance_power = 1.69 average_power = 1.03 wilson_b_weight_auto = False wilson_b_weight = None plain_pairs_radius = 5 refine_ap_and_dp = False b_iso_max = None } } group_occupancy { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False } group_anomalous { number_of_minimizer_cycles = 3 lbfgs_max_iterations = 20 number_of_finite_difference_tests = 0 } rigid_body { mode = *first_macro_cycle_only every_macro_cycle target = ls_wunit_k1 ml *auto target_auto_switch_resolution = 6 refine_rotation = True refine_translation = True max_iterations = 25 bulk_solvent_and_scale = True euler_angle_convention = *xyz zyz lbfgs_line_search_max_function_evaluations = 10 min_number_of_reflections = 100 multi_body_factor = 1 zone_exponent = 4 high_resolution = 3 max_low_high_res_limit = None number_of_zones = 5 } ncs { find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } find_automatically = True coordinate_sigma = None b_factor_weight = None excessive_distance_limit = None special_position_warnings_only = False restraint_group { reference = None selection = None coordinate_sigma = 0.05 b_factor_weight = 10 } restraint_group { reference = "chain A and (resseq 30:374 )" selection = "chain B and (resseq 30:374 )" coordinate_sigma = 0.05 b_factor_weight = 10 } } pdb_interpretation { apply_cif_modification { data_mod = None residue_selection = None } apply_cif_link { data_link = None residue_selection_1 = None residue_selection_2 = None } link_distance_cutoff = 3 disulfide_distance_cutoff = 3 chir_volume_esd = 0.2 peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None } nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 vdw_1_4_factor = 0.8 translate_cns_dna_rna_residue_names = None 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 { bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None } angle { action = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None angle_ideal = None sigma = None } } geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } ordered_solvent { low_resolution = 2.4 mode = auto filter_only *every_macro_cycle output_residue_name = "HOH" output_chain_id = "W" output_atom_name = "O" b_iso_min = 1 b_iso_max = 80 anisotropy_min = 0.1 b_iso = None scattering_type = "O" occupancy_min = 0.1 occupancy_max = 1 occupancy = 1 primary_map_type = "mFobs-DFmodel" primary_map_cutoff = 3.2 secondary_map_type = "2mFobs-DFmodel" secondary_map_cutoff = 1.2 h_bond_min_mac = 1.2 h_bond_min_sol = 1.2 h_bond_max = 3.2 new_solvent = *isotropic anisotropic refine_adp = True refine_occupancies = False filter_at_start = True n_cycles = 3 ignore_final_filtering_step = False } peak_search { use_sigma_scaled_maps = True resolution_factor = 0.25 map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6 min_peak_peak_dist = 1.8 use_hydrogens = False } max_number_of_peaks = 5232 peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 } } bulk_solvent_and_scale { bulk_solvent = True anisotropic_scaling = True k_sol_b_sol_grid_search = True minimization_k_sol_b_sol = True minimization_b_cart = False target = *ls_wunit_k1 ml symmetry_constraints_on_b_cart = True k_sol_max = 0.6 k_sol_min = 0 b_sol_max = 150 b_sol_min = 0 k_sol_grid_search_max = 0.6 k_sol_grid_search_min = 0 b_sol_grid_search_max = 80 b_sol_grid_search_min = 20 k_sol_step = 0.3 b_sol_step = 30 number_of_macro_cycles = 2 max_iterations = 25 min_iterations = 25 fix_k_sol = None fix_b_sol = None fix_b_cart { b11 = None b22 = None b33 = None b12 = None b13 = None b23 = None } apply_back_trace_of_b_cart = False verbose = -1 ignore_bulk_solvent_and_scale_failure = False } alpha_beta { free_reflections_per_bin = 140 number_of_macromolecule_atoms_absent = 225 n_atoms_included = 0 bf_atoms_absent = 15 final_error = 0 absent_atom_type = "O" method = *est calc estimation_algorithm = *analytical iterative verbose = -1 interpolation = False fix_scale_for_calc_option = None number_of_waters_absent = 613 sigmaa_estimator { kernel_width_free_reflections = 100 kernel_on_chebyshev_nodes = True number_of_sampling_points = 20 number_of_chebyshev_terms = 10 use_sampling_sum_weights = True } } mask { solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4 verbose = -1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True } cartesian_dynamics { temperature = 300 number_of_steps = 200 time_step = 0.0005 initial_velocities_zero_fraction = 0 n_print = 100 verbose = -1 } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 25 time_step = 0.0005 initial_velocities_zero_fraction = 0 interleaved_minimization { number_of_iterations = 0 time_step_factor = 10 restraints = *bonds *angles } n_print = 100 update_grads_shift = 0.3 refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first verbose = -1 } target_weights { wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None optimize_wxc = False optimize_wxu = False shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 } ias { b_iso_max = 100 occupancy_min = -1 occupancy_max = 1.5 ias_b_iso_max = 100 ias_b_iso_min = 0 ias_occupancy_min = 0.01 ias_occupancy_max = 3 initial_ias_occupancy = 1 build_ias_types = L R B BH use_map = True build_only = False file_prefix = None peak_search_map { map_type = *Fobs-Fmodel mFobs-DFmodel grid_step = 0.25 scaling = *volume sigma } } ls_target_names { target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \ ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \ ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \ ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \ lsm_k1ask3_fixed } twinning { twin_law = None detwin { mode = algebraic proportional *auto map_types { twofofc = *two_m_dtfo_d_fc two_dtfo_fc fofc = *m_dtfo_d_fc gradient m_gradient aniso_correct = False } } } structure_factors_and_gradients_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } r_free_flags { fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } }