[phenixbb] MR Rosetta Error

5 Aug 2013

      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]

HP: http://www.fas.ibaraki.ac.jp/?page_id=961

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~