December 2012 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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Memory and CPU usage
by Jon Agirre 05 Mar '13

05 Mar '13

Dear community, I'm planning on buying a new macbook for my first abroad postdoc venture, and I'm currently trying decide what amount of RAM & CPU to choose. My question is a little bit intricate: is there any rule of thumb to estimate the needed RAM versus the number of input atoms for any particular refinement type? I'm planning on tackling some big (18,000 residues/asu) refinements but I don't have any estimation as to how many GBs of RAM they might require. The maximum amount of RAM I can install is 16GB, but it is a non-standard configuration that might void Apple's warranty. About the CPU: how scalable are typical phenix processes? Would it be sensible to invest in a quad-core machine with HT? In this particular case, and since HT would present 8 logical cores, would I get any speed up from launching phenix tasks configured for 8 processors instead of 4? Thanks in advance! Jon

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use of the file find_ncs.resolve
by Fred. Vellieux 29 Jan '13

29 Jan '13

Hi all, I do not understand how the file "find_ncs.resolve" has to be fed into the "resolve" part of Phenix. Can it be used in the GUI for an autobuild procedure? Can anyone help on this? Ta very much in advance, F. Vellieux -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605 Fax: +33 438785494

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how to modify C-D bond length restraints in phenix?
by Maxime Cuypers 16 Jan '13

16 Jan '13

Hi, i am refining a perdeuterated neutron structure and have noticed a lot of positive density aside the D atoms on aliphatic and aromatic side chains. just in the alignment of C-D bonds (C-D then +), suggesting that phenix.refine constraints these bond lengths too short in my case. i tried automatic weights for geometry refinement and unrestrained specific C-D refinement but it is not satisfactory. then i found the following funny distances (angströms) in the pdb database neutron structures: 3KYX: program: Phenix.refine D-prot Distances: C-D aromatics = 0.93-0.94 C-D aliph. = 0.98 1CQ2 Program : xplor3.1 D-protein (despite the atoms being labelled as H according to abstract) Distances: C-D aromatics = 1.06-1.08 C-D aliph. = 1.08 4FC1 H-protein Distances: program: Phenix.refine C-H aromatics = 0.93 C-H aliph. = 0.97 1VCX H-protein program: CNS Distances: C-H aromatics = 1.06-1.10 C-H aliph. = 1.09 those neutron C-D/C-H bond lengths in pdb seem pretty much inconsistentto me. So it seems that phenix.refine uses C-D/ C-H bonds restrains that are different to other programs to below 1.0 Ang. ( ca. 0.10 A differences) how can i change the restraints to make it all longer bond lengths for C-D only? with a .cif file? i saw that phenix uses the CCP4 monomer library but the one in : /usr/local/phenix-.../chem_data/mon_lib/list only seem to be applying modifications. any clue on how to specifically modify the restraints parameters on C-D bonds would be very appreciated. Thanks, Maxime

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Macromolecular Crystallography School announcement : 2013 in Uruguay
by Alejandro Buschiazzo 16 Jan '13

16 Jan '13

Dear Colleagues, We are pleased to announce the *second Macromolecular Crystallography School 2013 *at the Institut Pasteur de Montevideo (Uruguay). All details can be found at www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013> *Title:* "Macromolecular Crystallography School 2013: From data processing to structure refinement and beyond" *Dates:*April 9th-17th, 2013. *Site:*Institut Pasteur de Montevideo (Montevideo), Uruguay *The workshop content:* Conceived to provide theoretical background and hands-on abilities in the use of computational tools to exploit X ray diffraction data. Through lectures, tutorials and hands-on trouble-shooting, the students will be trained in state-of-the-art macromolecular crystallography. Particular emphasis will be given to data processing, phasing/structure determination and model refinement/validation. The workshop will feature authors and experts of many modern crystallographic software packages. This workshop represents the continuation within the series started in 2010 (http://www.pasteur.edu.uy/mxcourse) on Macromolecular Crystallography. In this opportunity it is being co-organized by the Center for Structural Biology of the Mercosur CeBEM (www.cebem.org.ar <http://www.cebem.org.ar>), jointly with the Collaborative Computational Project Number 4 (CCP4 -- UK www.ccp4.ac.uk <http://www.ccp4.ac.uk>). Support from the Institut Pasteur International Network, the International Union of Crystallography and Institut Pasteur de Montevideo is also greatly acknowledged. *Applicants:* Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so they can be used during the workshop's hands-on sessions. There is no registration fee. Support for accommodation, per diem and local transportation will be provided to all participants from abroad. Support to cover travel expenses will be considered on a case-by-case basis. Specific requests should be well-grounded as we will only be able to select a limited number. *Application:* Application *deadline is February 10, 2013*. Application form, the program, contact info and other details can be found at www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013> Please address further inquiries to mx2013(a)pasteur.edu.uy <mailto:[email protected]> Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Problem with anomalous scattering factor refinement
by Subhani Bandara 27 Dec '12

27 Dec '12

Hi all, I've been trying to refine a structure with anomalous data with anomalous scattering factors. After some refinements without anomalous scattering factor refinement, I used the data.mtz file and original reflection file in reflection file editor to get the anomalous data merged with Rfree flags. When I tried to use this file with a pdb file (deleted hexadigest remark) and a cif file for ligands, the refinement ends with the following error at the end of the 3rd refinement cycle (I have only 3 cycles for a refinement). I was able to run a similar refinement with anomalous scattering factors for another structure without a problem. One difference in this structure is that this has NCS and the previous one didn't. I am using dev-1243 GUI. RuntimeError : scitbx array_family range error Traceback: File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/thread_utils.py", line 234, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py", line 87, in __call__ result = self.target() File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py", line 66, in __call__ result = self.run() File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py", line 69, in run refine_object = self._run(args, callback) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py", line 85, in _run call_back_handler=callback) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/command_line.py", line 169, in run map_manger.write_files() File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py", line 1735, in write_files map_coeff_dataset=self.write_mtz_file(), File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py", line 1724, in write_mtz_file pdb_hierarchy=self.refine_object.model.pdb_hierarchy()) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py", line 500, in __init__ pdb_hierarchy = pdb_hierarchy) File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py", line 428, in map_coefficients_from_fmodel sharp = params.sharpening).map_coeffs File "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/map_tools.py", line 55, in __init__ data = self.map_coeffs.data()*scale) Thanks in advance for any help Subhani

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Re: [phenixbb] problems with Rosetta_mr
by Yoni - UW 22 Dec '12

22 Dec '12

Thank you For you suggestions, Tom! Unfortunately I already ran the phenix.regression.wizard a few time, and actually also for the rebuild module only. This module seems to cause me all the troubles. It goes to the wrong .map file (compared with the provided log files of the tutorial) and have trouble reading the edited alignment file. I also tried to use the .eff files to run the failed steps only, with similar results. Another thing i think is worth mentioning is that I have a suspicion something is wrong with my installation of Phenix, because when I try to run "autobuild.creat 20 very good models" from the GUI it fails with an autobuild error, while working well with the command line. Thanks again, Yoni

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Excluding atoms from coordinate refinement ignored
by Engin Özkan 22 Dec '12

22 Dec '12

Hi Phenix developers, I have an issue using 1.8.1 (1168) with excluding atoms from coordinate refinement. I have defined a certain residue to be excluded from coordinate refinement, as can be seen in the .eff file produced by this run. refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous sites { individual = not (resseq 60 and resname PHE) torsion_angles = not (resseq 60 and resname PHE) rigid_body = None ... However, this gets ignored, and this residue and its NCS-related brethren get moved into nondescript electron density on a symmetry axis. This residue was just fine in an earlier version of Phenix, but when I switched to 1.8.1, it started moving into this density. So, I thought excluding it from xyz refinement, which is a dirty trick in my opinion, would fix this problem. Not so. I have the feeling that this is due to rotamer corrections as part of the torsion NCS implemented in 1.8.1 now. Sticking a zero occupancy dummy atom in the density did prevent this residue from moving in. Turning off torsion NCS also fixed it. By the way, I have "fix rotamer sidechains" off, as I am yet to see it improve things (at medium or low resolution). Thanks and happy holidays! Engin

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Problems with rosetta_mr
by Yoni Haitin 21 Dec '12

21 Dec '12

Hello all, I have been trying (desperetly) to run the Rosetta_MR. I have encountered some problems with my data, so I switched to the "HNP3-mr-rosetta" tutorial dataset. I followd the debugging suggestions in the instructions webpage with no improvement. It seems that I have a problem in the rebuild stage. Attached are the RUN_FILE_1.log from REBUILD_IN_SETS_5 and ../WORK_1/rebuild.log. The edited_align.ali file cannot be opened for some reason. Another issue is that the map used is being taken from "overall_best_denmod_map_coeffs_nf.map" instead of "cycle_best" (as is in the tutorial's mr_rosetta_output log). this seems to produce an error (last log file attached). What should I do next? Thank you, Yoni Parameters taken from: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/PARAMS_1.eff # mr_rosetta_rebuild # # Run automr mr_rosetta_rebuild with rosetta # Type phenix.doc for help Values of all params: mr_rosetta_rebuild { input_files { model = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb" map = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map" seq_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/EDITED_1dfn.seq" hhr_files = None alignment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali" model_info_file = "" fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_09_05.200_v1_3.gz" fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_03_05.200_v1_3.gz" 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_rebuild.log" params_out = "mr_rosetta_rebuild_params.eff" } directories { temp_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" workdir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" gui_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta" top_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14" rosetta_path = "/Users/administrator/rosetta_3.4" rosetta_binary_dir = "rosetta_source/bin" rosetta_binary_name = "mr_protocols.default.macosgccrelease" 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" } 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 = 20 chunk_size = 1 edit_model = True superpose_model = False } 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 21 21 2" chain_type = *PROTEIN DNA RNA ncs_copies = 1 } 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 = True ignore_errors_in_subprocess = True check_run_command = False max_wait_time = 100 wait_between_submit_time = 1 wizard_directory_number = 14 n_dir_max = 100000 number_to_print = 5 write_run_directory_to_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/INFO_FILE_1" 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 } non_user_params { file_base = "1zmm_mr.1" print_citations = False highest_id = 10 is_sub_process = True dummy_autobuild = False dummy_refinement = False dummy_rosetta = False prerefine_only = False skip_clash_guard = True correct_special_position_tolerance = None comparison_mtz = "" labin_comparison_mtz = None write_local_files = False rosetta_fixed_seed = None } } Starting mr_rosetta_rebuild Date: Thu Dec 20 14:44:49 2012 Directory: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5 HOST = ZagottasMacPro.local HOSTTYPE = intel-mac MACHTYPE = x86_64 OSTYPE = darwin VENDOR = apple USER = administrator PID = 36828 Checking rosetta paths: rosetta binary: /Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease database_dir: /Users/administrator/rosetta_3.4/rosetta_database script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/public/electron_density pilot_script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/pilot/frank/ Changing to work directory: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1 Rebuilding the model /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb with rosetta Rebuilding model using map at resolution of 3.0 A Generating 20 rebuilt models ================================================================================ Reading model from /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb ================================================================================ ALIGNMENT LINES: ## TARGET 1zmm_ # hhsearch scores_from_program: 0 1.00 0 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 1 -CYCRIPACIAGERRYGTCIYQGRLWAFCC -- Trying to adjust the PDB sequence from alignment file: -CYCRIPACIAGERRYGTCIYQGRLWAFCC to match the actual PDB sequence: YCRIPACIAGERRYGTCIYQGRLWAFCC New alignment line 4 for PDB: 1 --YCRIPACIAGERRYGTCIYQGRLWAFCC Start position of target sequence in sequence file: 0 Aligned model for comparison: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** --- Here is ../WORK_1/rebuild.log: core.init: Mini-Rosetta version unknown from unknown core.init: command: /Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=345021854 seed_offset=0 real_seed=345021854 core.init.random: RandomGenerator:init: Normal mode, seed=345021854 RG_type=mt19937 ERROR: Warning: can't open file /Users/administrator/Yoni/Rosettal/ tutorial/ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali! ERROR:: Exit from: src/core/sequence/util.cc line: 380 --- core.init: Mini-Rosetta version exported from unknown core.init: command: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_source/bin/mr_protocols.default.macosgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-340184367 seed_offset=0 real_seed=-340184367 core.init.random: RandomGenerator:init: Normal mode, seed=-340184367 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pdb_pair_stats_fine core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_n core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_pp core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/Rama_smooth_dyn.dat_ss_6.4 core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/env_log.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cbeta_den.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pair_log.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cenpack_log.txt core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.electron_density.ElectronDensity: Loading Density Map core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map /Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map. Not loading map. core.scoring.electron_density.ElectronDensity: [ ERROR ] Error loading density map named '/Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map' -- Yoni Haitin, Ph.D. Department of Physiology and Biophysics University of Washington Seattle, WA 98195-7290 Email: yonihaitin(a)gmail.com Email(2): haitinyo(a)uw.edu

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