October 2011 - phenixbb - phenix-online.org

STOPWIZARD
by Morten Grøftehauge 17 Oct '11

17 Oct '11

Dear phenixbb, The Phenix manual mentions several times that making a file named STOPWIZARD in the wizard root directory will stop the wizard in an orderly fashion the next time it checks for STOPWIZARD. There is however no mention of how to properly restart the wizard after having stopped it... How? I seem to remember something about it being >phenix.appropriate_wizard params_used_in_wizard.eff but I'd like be sure that I don't simply start over by doing that. Also can I then change the parameters before restarting the wizard? Say, hypothetically of course, that I've started mr.rosetta and asked for 1000 prerefined models and realised that it will take ridiculously long and be rather redundant since I specified both the .hhr file from global and local alignment and the top hit has two chains (resulting in mr.rosetta wanting to build 4000 prerefined models) but I don't want to throw away the 700 models already built. Could I do something about that? Sincerely, Morten Grøftehauge, PhD Durham University

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mr_rosetta memory usage
by Tjaard Pijning 17 Oct '11

17 Oct '11

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 } }

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re-building chains
by Leonid Sazanov 14 Oct '11

14 Oct '11

Hi, how exactly can one tell Autobuild to rebuild-in-place chains A and B from the input model, but build chain C de-novo? If I give it list of chains to re-build (rebuild_near_chain="A B" in GUI, dev-874 version), what happens is that either all chains are rebuild-in-place (if rebuild-in-place=True) or all chains are built de-novo (if rebuild-in-place=False). Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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1.7.2 slow to open
by Jinsong Liu 12 Oct '11

12 Oct '11

Hi there, I wonder if there is anyone else experiencing a VERY VERY slow opening of the phenix GUI for the latest version of 1.7.2? We have RHEL 5.3 and CentOS 5.6, both machines show this. Most of the time, it will take minutes, sometime more than 10 minutes. There is no any warning or error message, after the long waiting the GUI will suddenly show up. In the older version, it usually takes seconds to load the GUI. Thanks. Jinsong -- Jinsong Liu, Ph.D. Principle Investigator & Head of Laboratory of Structural Biology Guangzhou Institute of Biomedicine and Health (GIBH) Chinese Academy of Sciences Guangzhou ( Canton ) 510630, China Phone: 86-20-32015317 (Office) E-mail: liu_jinsong(a)gibh.ac.cn

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Re: [phenixbb] mr_rosetta
by Thomas C. Terwilliger 11 Oct '11

11 Oct '11

Hi Abhinav, This format is very unforgiving. It has to have exactly 5 lines: ## TARGET SP_3n91 # hhsearch scores_from_program: 0 1.00 0 --DDDEVTMNSK.... 0 GSDNEFPDFDYQ.... -- also note I changed SP 3n91 to SP_3n91. Your PDB file name must also start with SP_3n91 in this case. You need a pdb file name with at least 5 chars before the ".pdb" and these 5 characters have to match the 5 characters after TARGET on the first line. Note that the other format read by mr_rosetta is a lot easier: > title text for sequence of target to follow VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD > title text for sequence of template (supplied PDB) to follow -AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG All the best, Tom T >> Somebody helped me out with the format. Thanks. >> My alignment file looks like: >> ## SP 3n91 >> >> >> 0 --DDDEVTMNSK.... >> 0 GSDNEFPDFDYQ.... >> >> >> >> But phenix says >> >> ******************* ERROR ENDING *************** >> >> Sorry, the alignment file ['xx.ali'] >> does not seem to have the correct format? >> It can either start with '##' or with '> title of target seq here' >> >> ******************* ERROR ENDING *************** >> >> I do have the file starting with '##'! >> >> Thanks, >> Abhinav >> >> JCSG@SSRL, SLAC >> Phone: (650) 926-2992 >> Fax: (650) 926-3292 >> >> >> On 10/11/2011 12:23 PM, Abhinav Kumar wrote: >>> Hi, >>> >>> I am looking for file format for alignment file (*.ali) used in >>> mr_rosetta. >>> The description on the Phenix web site is not clear. >>> Can someone please describe the file format with an example? >>> -- >>> >>> Thanks, >>> Abhinav >>> >>> JCSG@SSRL, SLAC >>> Phone: (650) 926-2992 >>> Fax: (650) 926-3292 >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] mr_rosetta
by Thomas C. Terwilliger 11 Oct '11

11 Oct '11

Hi Abhinav, Here is an example. > cat WORK_1/alignment.ali ## TARGET coord # hhsearch scores_from_program: 0 1.00 0 AQLMDMRD 0 AQLMDMRD -- (the -- at the end is included in the file) You can also use one with just 4 lines (sculptor format): > title text for sequence of target to follow VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD > title text for sequence of template (supplied PDB) to follow -AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG All the best, Tom T >> Hi, >> >> I am looking for file format for alignment file (*.ali) used in >> mr_rosetta. >> The description on the Phenix web site is not clear. >> Can someone please describe the file format with an example? >> -- >> >> Thanks, >> Abhinav >> >> JCSG@SSRL, SLAC >> Phone: (650) 926-2992 >> Fax: (650) 926-3292 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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mr_rosetta
by Abhinav Kumar 11 Oct '11

11 Oct '11

Hi, I am looking for file format for alignment file (*.ali) used in mr_rosetta. The description on the Phenix web site is not clear. Can someone please describe the file format with an example? -- Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292

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Re: [phenixbb] phenix.mr_rosetta not running "prerefine"
by Thomas C. Terwilliger 11 Oct '11

11 Oct '11

Hi Laurie, The problem is that mr_rosetta needed a pdb file name with more than 4 characters before the ".pdb" for this shortcut of generating pre-refined models to work (the Rosetta routine requires a longer file name). So if you rename your PDB file this should run (it does on my machine.) I will fix mr_rosetta so that it can take your PDB file. All the best, Tom T >> On Tue, Oct 11, 2011 at 12:33 PM, Thomas C. Terwilliger < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Laurie, >>> >>> Yes, it is not doing anything. There is something that didn't work in >>> the >>> inputs. Can you send me your fasta and PDB files and I'll just run it >>> here >>> to see what is wrong? >>> >>> Thanks! >>> -Tom T >>> >>> >> OK - I am also sending: >>> >> >>> >> >>> /netscr/bettsl/rosetta_test/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log >>> >> >>> >> On Tue, Oct 11, 2011 at 12:01 PM, Thomas C. Terwilliger < >>> >> terwilliger(a)lanl.gov> wrote: >>> >> >>> >>> Hi Laurie, >>> >>> >>> >>> Yes, something didn't work it all right. Can you send me, off-list, >>> this >>> >>> log file: >>> >>> >>> >>> >>> >>> >>> /netscr/bettsl/rosetta_test/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log >>> >>> >>> >>> which I am guessing has some kind of error message in it. >>> >>> >>> >>> Thanks! >>> >>> -Tom T >>> >>> >>> >>> >> Hi - I tried the little prerefine without any data script in your >>> >>> >> documentation - I don't think it's working right. I attach the >>> >>> script >>> >>> >> file >>> >>> >> that I made (prerefine.dat) and the RUN_FILE_1.log. >>> >>> >> >>> >>> >> I can send more info offline if need be. >>> >>> >> >>> >>> >> Thanks >>> >>> >> >>> >>> >> LAurie Betts >>> >>> >> _______________________________________________ >>> >>> >> phenixbb mailing list >>> >>> >> phenixbb(a)phenix-online.org >>> >>> >> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >>> >>> >>> >>> _______________________________________________ >>> >>> phenixbb mailing list >>> >>> phenixbb(a)phenix-online.org >>> >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >>> >> >>> >>> >>

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refinements settings .eff
by Christian Roth 11 Oct '11

11 Oct '11

Hi Phenix gurus, I have done a refinement with an sodium ion. I had generated a phil file for the distance restraints to the surrounding water. Now i am not sure if it is really there. I removed it and removed the phil from the list in the gui. Now phenix complains about no Atom selected and stops. In the .eff file all restraints are incorporated and in I deleted therefore the geometric restraints manually from the . eff file. As a consequence an unused parameter warning appears about unused parameters or spelling errors in the input file. I guess the .eff file. My default parameter folder is empty. Does phenix load the .eff file from the previous run and would it help to remove this? I dont wanne start a new project just to be in the default configuration mode without additional information in the .eff file. I did this using the gui so I am not sure how to incorporate the --unused_ok command to which may help to convince phenix to process the job. I hope it is clear what I mean and thanks for any suggestion. Christian

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phenix.mr_rosetta not running "prerefine"
by Laurie Betts 11 Oct '11

11 Oct '11

Hi - I tried the little prerefine without any data script in your documentation - I don't think it's working right. I attach the script file that I made (prerefine.dat) and the RUN_FILE_1.log. I can send more info offline if need be. Thanks LAurie Betts

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