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