Hi,

 

I am currently running mr_rosetta and found that after a while the computer (running OpenSuse/linux) slows down dramatically because its memory (8 GB) is running full. I’m not sure if the program still runs or not.

Is there a way to limit the amount of memory that phenix/mr_rosetta uses ? Or should I e.g. lower the amount of models being used (currently 5) ?

(Before starting mr_rosetta I ran the regression test which was fine).

 

Kind regards,

 

Tjaard Pijning

University of Groningen

 

This is the parameter file :

 

mr_rosetta {

  input_files {

    seq_file = gEP_mature.txt"

    hhr_files = "051011_3011840.hhr"

    alignment_files = None

    model_info_file = ""

    data = "XDS_ASCII_C2221.mtz"

    labin = None

    search_models = None

    copies_in_search_models = None

    mr_rosetta_solutions = ""

    ids_to_load = None

    map_coeffs = ""

    labin_map_coeffs = None

    map = ""

    display_solutions = False

    fragment_files = "aat000_03_05.200_v1_3"

    fragment_files = "aat000_09_05.200_v1_3"

    use_dummy_fragment_files = False

    sort_fragment_files = True

  }

  output_files {

    log = "mr_rosetta.log"

    params_out = "mr_rosetta_params.eff"

  }

  directories {

    temp_dir = "mr_rosetta/MR_ROSETTA_7/WORK_1"

    workdir = "mr_rosetta/MR_ROSETTA_7"

    output_dir = "mr_rosetta"

    top_output_dir = "mr_rosetta/MR_ROSETTA_7"

    rosetta_path = ""

    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 = 5

    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 = 300

    selection_criteria_rot_value = 75

    fast_search_mode = True

    search_down_percent = 25

    mr_resolution = 3

    refine_after_mr = True

    denmod_after_refine = True

    find_ncs_after_mr = True

    min_length_ncs = 10

    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 = None

    chain_type = *PROTEIN DNA RNA

    ncs_copies = 2

  }

  control {

    verbose = False

    debug = False

    raise_sorry = False

    dry_run = False

    nproc = 5

    group_run_command = "sh "

    condor = None

    single_run_command = "sh "

    background = None

    ignore_errors_in_subprocess = True

    check_run_command = False

    max_wait_time = 100

    wait_between_submit_time = 1

    n_dir_max = 100000

    number_to_print = 5

    write_run_directory_to_file = 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

  }

  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

    skip_clash_guard = True

    correct_special_position_tolerance = None

    comparison_mtz = ""

    labin_comparison_mtz = None

    write_local_files = False

    rosetta_fixed_seed = None

  }

}