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</o:shapelayout></xml><![endif]--></head><body lang=JA link=blue vlink=purple style='text-justify-trim:punctuation'><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'>Dear all<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'>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></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'>When I performed Rosetta MR via Phenix, I received the Error message as follows:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'>What is wrong? What should I do to solve the problem? I use Ubuntu 12.10 as a platform.<o:p></o:p></span></p><div style='mso-element:para-border-div;border-top:solid windowtext 3.0pt;border-left:none;border-bottom:solid windowtext 3.0pt;border-right:none;padding:1.0pt 0mm 1.0pt 0mm'><p class=MsoPlainText style='margin-bottom:12.0pt;border:none;padding:0mm'><span lang=EN-US style='font-family:"MS Gothic"'>Starting mr_rosetta<br>Date: Mon Aug 5 11:06:04 2013 <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></div><p class=MsoNormal><span lang=EN-US>Best regards<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Masaki UNNO, Ph.D.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Frotier Research Center for Applied Atomic Sciences,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Ibaraki University<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Ibaraki Quantum Beam Research Center<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Tel: 029-352-3239, Fax: 029-287-7872<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>E-mail: unno19@mx.ibaraki.ac.jp<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>HP: http://www.fas.ibaraki.ac.jp/?page_id=961<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>