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[(a)]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
}
}
