[phenixbb] MR Rosetta Error
Terwilliger, Thomas C
terwilliger at lanl.gov
Mon Aug 5 09:58:31 PDT 2013
Hi Masaki,
I think that if you will specify a sequence file then this problem may be fixed. I am sorry for the useless error message and I'll fix that!
Let me know if that does not do it!
All the best,
Tom T
On Aug 4, 2013, at 11:55 PM, Masaki UNNO wrote:
Dear all
I am trying to determine a protein structure using Rosetta MR. It is the first time to use Rosetta (Phenix).
When I performed Rosetta MR via Phenix, I received the Error message as follows:
What is wrong? What should I do to solve the problem? I use Ubuntu 12.10 as a platform.
Starting mr_rosetta
Date: Mon Aug 5 11:06:04 2013
Directory: /home/pad1/Work/20130222_PF/PAD1034/PHENIX/REF01/MR_ROSETTA_1
mr_rosetta {
input_files {
seq_file = ""
hhr_files = None
alignment_files = None
model_info_file = ""
data = "/home/pad1/Work/20130222_PF/PAD1034/process/PAD1034_NW12A_P61_scale2.mtz"
data_labels = "F_PAD1034,SIGF_PAD1034"
free_r_data = ""
free_r_labels = "FreeR_flag"
labin = None
search_models = "/home/pad1/Work/20130222_PF/PAD1034/MR/PAD4_Arg_cut.pdb"
copies_in_search_models = None
mr_rosetta_solutions = ""
ids_to_load = None
map_coeffs = ""
labin_map_coeffs = None
map = ""
refinement_params = ""
display_solutions = False
fragment_files = None
fragment_files_chain_list = None
fragment_files_9_mer_by_chain = None
fragment_files_3_mer_by_chain = None
use_dummy_fragment_files = False
sort_fragment_files = True
}
output_files {
log = "mr_rosetta.log"
params_out = "mr_rosetta_params.eff"
}
directories {
temp_dir = "/home/pad1/Work/20130222_PF/PAD1034/PHENIX/REF01/MR_ROSETTA_1/WORK_1"
workdir = "/home/pad1/Work/20130222_PF/PAD1034/PHENIX/REF01/MR_ROSETTA_1"
output_dir = "/home/pad1/Work/20130222_PF/PAD1034/PHENIX/REF01"
gui_output_dir = "/home/pad1/Work/20130222_PF/PAD1034/PHENIX/REF01"
top_output_dir = "/home/pad1/Work/20130222_PF/PAD1034/PHENIX/REF01/MR_ROSETTA_1"
rosetta_path = "/home/unno19-frt/programs/rosetta-3.5"
rosetta_binary_dir = "rosetta_source/bin"
rosetta_binary_name = "mr_protocols.default"
rosetta_script_dir = "rosetta_source/src/apps/public/electron_density"
rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/"
rosetta_database_dir = "rosetta_database"
}
read_hhpred {
number_of_models = 1
number_of_models_to_skip = 0
copies_to_extract = None
only_extract_proper_symmetry = False
}
place_model {
run_place_model = True
prerefine {
run_prerefine = False
number_of_prerefine_models = 1000
number_of_models_in_ensemble = 1
}
model_already_placed = False
model_already_aligned = False
number_of_output_models = 5
align_with_sculptor = True
identity = None
identity_for_scoring_only = 25
use_all_plausible_sg = True
overlap_allowed = 10
selection_criteria_rot_value = 75
fast_search_mode = True
search_down_percent = 25
mr_resolution = 4.2
refine_after_mr = True
denmod_after_refine = True
ps_in_rebuild = False
find_ncs_after_mr = True
min_length_ncs = 10
fixed_model = ""
fixed_model_identity = None
fixed_ensembles {
fixed_ensembleID_list = None
fixed_euler_list = 0 0 0
fixed_frac_list = 0 0 0
fixed_frac_list_is_fractional = True
}
copies_of_search_model_to_place = None
}
rescore_mr {
run_rescore_mr = True
nstruct = 5
relax = False
include_unrelaxed_in_scoring = False
align = True
edit_model = False
stage_to_rescore = "mr_solution"
}
rosetta_rebuild {
run_rosetta_rebuild = True
stage_to_rebuild = "rescored_mr_solution"
max_solutions_to_rebuild = 5
min_solutions_to_rebuild = 1
llg_percent_of_max_to_keep = 50
rosetta_models = 100
chunk_size = 1
edit_model = True
superpose_model = False
}
rosetta_rescore {
run_rosetta_rescore = True
percentage_to_rescore = 20
min_solutions_to_rescore = 2
}
similarity {
run_similarity = False
required_cc = 0.2
number_of_required_cc = 5
}
refine_top_models {
run_refine_top_models = True
stage_to_refine = None
sort_score_type = None
percent_to_refine = 20
denmod_after_refine = True
}
average_density_top_models {
run_average_density_top_models = True
percent_to_average = 100
}
relax_top_models {
run_relax_top_models = True
stage_to_relax = None
number_to_relax = 2
nstruct = 5
}
autobuild_top_models {
run_autobuild_top_models = True
number_to_autobuild = 2
quick = False
phase_and_build = False
macro_cycles = None
morph = False
edit_model = True
use_map_coeffs = True
}
setup_repeat_mr_rosetta {
run_setup_repeat_mr_rosetta = True
repeats = 1
template_repeats = 0
morph_repeats = 0
number_to_repeat = 1
acceptable_r = 0.25
minimum_delta_r = None
}
repeat_mr_rosetta {
run_repeat_mr_rosetta = True
copies_in_new_search_group = 1
update_map_coeffs_with_autobuild = True
}
rosetta_modeling {
map_resolution = 3
map_grid_spacing = 1.5
map_weight = 1
map_window = 5
include_solvation_energy = True
weights_file = ""
}
crystal_info {
resolution = 0
space_group = "P 61"
chain_type = *PROTEIN DNA RNA
ncs_copies = Auto
}
control {
verbose = False
debug = False
raise_sorry = False
dry_run = False
nproc = 1
group_run_command = "sh "
queue_commands = None
condor_universe = "vanilla"
add_double_quotes_in_condor = True
condor = None
one_subprocess_level = None
single_run_command = "sh "
last_process_is_local = True
background = None
ignore_errors_in_subprocess = True
check_run_command = False
max_wait_time = 100
wait_between_submit_time = 1
wizard_directory_number = 1
n_dir_max = 100000
number_to_print = 5
write_run_directory_to_file = None
rosetta_command = None
resolve_command_list = None
start_point = *place_model rescore_mr rosetta_rebuild rosetta_rescore \
similarity refine_top_models average_density_top_models \
relax_top_models autobuild_top_models \
setup_repeat_mr_rosetta repeat_mr_rosetta
stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \
similarity refine_top_models average_density_top_models \
relax_top_models autobuild_top_models \
setup_repeat_mr_rosetta repeat_mr_rosetta
clean_up = False
add_id = True
}
non_user_params {
file_base = None
print_citations = True
highest_id = 0
is_sub_process = False
dummy_autobuild = False
dummy_refinement = False
dummy_rosetta = False
prerefine_only = False
skip_clash_guard = True
correct_special_position_tolerance = None
ncs_in_refinement = *torsion cartesian None
comparison_mtz = ""
labin_comparison_mtz = None
write_local_files = False
rosetta_fixed_seed = None
}
}
Best regards
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Masaki UNNO, Ph.D.
Frotier Research Center for Applied Atomic Sciences,
Ibaraki University
Ibaraki Quantum Beam Research Center
162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
Tel: 029-352-3239, Fax: 029-287-7872
E-mail: unno19 at mx.ibaraki.ac.jp<mailto:unno19 at mx.ibaraki.ac.jp>
HP: http://www.fas.ibaraki.ac.jp/?page_id=961
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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