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: [email protected]mailto:[email protected] HP: http://www.fas.ibaraki.ac.jp/?page_id=961 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb