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<DIV>Hi,</DIV>
<DIV> </DIV>
<DIV>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.</DIV>
<DIV>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) ?</DIV>
<DIV>(Before starting mr_rosetta I ran the regression test which was
fine).</DIV>
<DIV> </DIV>
<DIV>Kind regards,</DIV>
<DIV> </DIV>
<DIV>Tjaard Pijning</DIV>
<DIV>University of Groningen</DIV>
<DIV> </DIV>
<DIV>This is the parameter file :</DIV>
<DIV> </DIV>
<DIV>mr_rosetta {</DIV>
<DIV> input_files {</DIV>
<DIV> seq_file = gEP_mature.txt"</DIV>
<DIV> hhr_files = "051011_3011840.hhr"</DIV>
<DIV> alignment_files = None</DIV>
<DIV> model_info_file = ""</DIV>
<DIV> data = "XDS_ASCII_C2221.mtz"</DIV>
<DIV> labin = None</DIV>
<DIV> search_models = None</DIV>
<DIV> copies_in_search_models = None</DIV>
<DIV> mr_rosetta_solutions = ""</DIV>
<DIV> ids_to_load = None</DIV>
<DIV> map_coeffs = ""</DIV>
<DIV> labin_map_coeffs = None</DIV>
<DIV> map = ""</DIV>
<DIV> display_solutions = False</DIV>
<DIV> fragment_files = "aat000_03_05.200_v1_3"</DIV>
<DIV> fragment_files = "aat000_09_05.200_v1_3"</DIV>
<DIV> use_dummy_fragment_files = False</DIV>
<DIV> sort_fragment_files = True</DIV>
<DIV> }</DIV>
<DIV> output_files {</DIV>
<DIV> log = "mr_rosetta.log"</DIV>
<DIV> params_out = "mr_rosetta_params.eff"</DIV>
<DIV> }</DIV>
<DIV> directories {</DIV>
<DIV> temp_dir = "mr_rosetta/MR_ROSETTA_7/WORK_1"</DIV>
<DIV> workdir = "mr_rosetta/MR_ROSETTA_7"</DIV>
<DIV> output_dir = "mr_rosetta"</DIV>
<DIV> top_output_dir = "mr_rosetta/MR_ROSETTA_7"</DIV>
<DIV> rosetta_path = ""</DIV>
<DIV> rosetta_binary_dir = "rosetta_source/bin"</DIV>
<DIV> rosetta_binary_name = "mr_protocols.default"</DIV>
<DIV> rosetta_script_dir =
"rosetta_source/src/apps/public/electron_density"</DIV>
<DIV> rosetta_pilot_script_dir =
"rosetta_source/src/apps/pilot/frank/"</DIV>
<DIV> rosetta_database_dir = "rosetta_database"</DIV>
<DIV> }</DIV>
<DIV> read_hhpred {</DIV>
<DIV> number_of_models = 5</DIV>
<DIV> number_of_models_to_skip = 0</DIV>
<DIV> copies_to_extract = None</DIV>
<DIV> only_extract_proper_symmetry = False</DIV>
<DIV> }</DIV>
<DIV> place_model {</DIV>
<DIV> run_place_model = True</DIV>
<DIV> prerefine {</DIV>
<DIV> run_prerefine = False</DIV>
<DIV> number_of_prerefine_models = 1000</DIV>
<DIV> number_of_models_in_ensemble = 1</DIV>
<DIV> }</DIV>
<DIV> model_already_placed = False</DIV>
<DIV> model_already_aligned = False</DIV>
<DIV> number_of_output_models = 5</DIV>
<DIV> align_with_sculptor = True</DIV>
<DIV> identity = None</DIV>
<DIV> identity_for_scoring_only = 25</DIV>
<DIV> use_all_plausible_sg = True</DIV>
<DIV> overlap_allowed = 300</DIV>
<DIV> selection_criteria_rot_value = 75</DIV>
<DIV> fast_search_mode = True</DIV>
<DIV> search_down_percent = 25</DIV>
<DIV> mr_resolution = 3</DIV>
<DIV> refine_after_mr = True</DIV>
<DIV> denmod_after_refine = True</DIV>
<DIV> find_ncs_after_mr = True</DIV>
<DIV> min_length_ncs = 10</DIV>
<DIV> fixed_ensembles {</DIV>
<DIV> fixed_ensembleID_list = None</DIV>
<DIV> fixed_euler_list = 0 0 0</DIV>
<DIV> fixed_frac_list = 0 0 0</DIV>
<DIV> fixed_frac_list_is_fractional = True</DIV>
<DIV> }</DIV>
<DIV> copies_of_search_model_to_place = None</DIV>
<DIV> }</DIV>
<DIV> rescore_mr {</DIV>
<DIV> run_rescore_mr = True</DIV>
<DIV> nstruct = 5</DIV>
<DIV> relax = False</DIV>
<DIV> include_unrelaxed_in_scoring = False</DIV>
<DIV> align = True</DIV>
<DIV> edit_model = False</DIV>
<DIV> stage_to_rescore = "mr_solution"</DIV>
<DIV> }</DIV>
<DIV> rosetta_rebuild {</DIV>
<DIV> run_rosetta_rebuild = True</DIV>
<DIV> stage_to_rebuild = "rescored_mr_solution"</DIV>
<DIV> max_solutions_to_rebuild = 5</DIV>
<DIV> min_solutions_to_rebuild = 1</DIV>
<DIV> llg_percent_of_max_to_keep = 50</DIV>
<DIV> rosetta_models = 100</DIV>
<DIV> chunk_size = 1</DIV>
<DIV> edit_model = True</DIV>
<DIV> superpose_model = False</DIV>
<DIV> }</DIV>
<DIV> rosetta_rescore {</DIV>
<DIV> run_rosetta_rescore = True</DIV>
<DIV> percentage_to_rescore = 20</DIV>
<DIV> min_solutions_to_rescore = 2</DIV>
<DIV> }</DIV>
<DIV> similarity {</DIV>
<DIV> run_similarity = False</DIV>
<DIV> required_cc = 0.2</DIV>
<DIV> number_of_required_cc = 5</DIV>
<DIV> }</DIV>
<DIV> refine_top_models {</DIV>
<DIV> run_refine_top_models = True</DIV>
<DIV> stage_to_refine = None</DIV>
<DIV> sort_score_type = None</DIV>
<DIV> percent_to_refine = 20</DIV>
<DIV> denmod_after_refine = True</DIV>
<DIV> }</DIV>
<DIV> average_density_top_models {</DIV>
<DIV> run_average_density_top_models = True</DIV>
<DIV> percent_to_average = 100</DIV>
<DIV> }</DIV>
<DIV> relax_top_models {</DIV>
<DIV> run_relax_top_models = True</DIV>
<DIV> stage_to_relax = None</DIV>
<DIV> number_to_relax = 2</DIV>
<DIV> nstruct = 5</DIV>
<DIV> }</DIV>
<DIV> autobuild_top_models {</DIV>
<DIV> run_autobuild_top_models = True</DIV>
<DIV> number_to_autobuild = 2</DIV>
<DIV> quick = False</DIV>
<DIV> phase_and_build = False</DIV>
<DIV> macro_cycles = None</DIV>
<DIV> morph = False</DIV>
<DIV> edit_model = True</DIV>
<DIV> use_map_coeffs = True</DIV>
<DIV> }</DIV>
<DIV> setup_repeat_mr_rosetta {</DIV>
<DIV> run_setup_repeat_mr_rosetta = True</DIV>
<DIV> repeats = 1</DIV>
<DIV> template_repeats = 0</DIV>
<DIV> morph_repeats = 0</DIV>
<DIV> number_to_repeat = 1</DIV>
<DIV> acceptable_r = 0.25</DIV>
<DIV> minimum_delta_r = None</DIV>
<DIV> }</DIV>
<DIV> repeat_mr_rosetta {</DIV>
<DIV> run_repeat_mr_rosetta = True</DIV>
<DIV> copies_in_new_search_group = 1</DIV>
<DIV> update_map_coeffs_with_autobuild = True</DIV>
<DIV> }</DIV>
<DIV> rosetta_modeling {</DIV>
<DIV> map_resolution = 3</DIV>
<DIV> map_grid_spacing = 1.5</DIV>
<DIV> map_weight = 1</DIV>
<DIV> map_window = 5</DIV>
<DIV> include_solvation_energy = True</DIV>
<DIV> weights_file = ""</DIV>
<DIV> }</DIV>
<DIV> crystal_info {</DIV>
<DIV> resolution = 0</DIV>
<DIV> space_group = None</DIV>
<DIV> chain_type = *PROTEIN DNA RNA</DIV>
<DIV> ncs_copies = 2</DIV>
<DIV> }</DIV>
<DIV> control {</DIV>
<DIV> verbose = False</DIV>
<DIV> debug = False</DIV>
<DIV> raise_sorry = False</DIV>
<DIV> dry_run = False</DIV>
<DIV> nproc = 5</DIV>
<DIV> group_run_command = "sh "</DIV>
<DIV> condor = None</DIV>
<DIV> single_run_command = "sh "</DIV>
<DIV> background = None</DIV>
<DIV> ignore_errors_in_subprocess = True</DIV>
<DIV> check_run_command = False</DIV>
<DIV> max_wait_time = 100</DIV>
<DIV> wait_between_submit_time = 1</DIV>
<DIV> n_dir_max = 100000</DIV>
<DIV> number_to_print = 5</DIV>
<DIV> write_run_directory_to_file = None</DIV>
<DIV> resolve_command_list = None</DIV>
<DIV> start_point = *place_model rescore_mr rosetta_rebuild
rosetta_rescore \</DIV>
<DIV>
similarity refine_top_models average_density_top_models \</DIV>
<DIV>
relax_top_models autobuild_top_models \</DIV>
<DIV>
setup_repeat_mr_rosetta repeat_mr_rosetta</DIV>
<DIV> stop_point = place_model rescore_mr rosetta_rebuild
rosetta_rescore \</DIV>
<DIV>
similarity refine_top_models average_density_top_models \</DIV>
<DIV>
relax_top_models autobuild_top_models \</DIV>
<DIV>
setup_repeat_mr_rosetta repeat_mr_rosetta</DIV>
<DIV> }</DIV>
<DIV> non_user_params {</DIV>
<DIV> file_base = None</DIV>
<DIV> print_citations = True</DIV>
<DIV> highest_id = 0</DIV>
<DIV> is_sub_process = False</DIV>
<DIV> dummy_autobuild = False</DIV>
<DIV> dummy_refinement = False</DIV>
<DIV> dummy_rosetta = False</DIV>
<DIV> skip_clash_guard = True</DIV>
<DIV> correct_special_position_tolerance = None</DIV>
<DIV> comparison_mtz = ""</DIV>
<DIV> labin_comparison_mtz = None</DIV>
<DIV> write_local_files = False</DIV>
<DIV> rosetta_fixed_seed = None</DIV>
<DIV> }</DIV>
<DIV>}</DIV></DIV></DIV></BODY></HTML>