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problem with refinement in AutoBuild
by Michael Thompson 15 Aug '13

15 Aug '13

Hello Everyone, I am having a problem running autobuild, which appears to be happening during the refinement step. I start autobuild using : phenix.autobuild data=data.mtz model=model.mtz seq_file=sequence.dat rebuild_from_fragments=True i_ran_seed=124889 find_ncs=False refine_with_ncs=False nproc=4 The runs are failing during the first cycle with the following error message: AutoBuild_build_cycle AutoBuild Run 2 Thu Aug 15 13:37:34 2013 Build cycle 1 of 16 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using NO_LIG_NO_WAT_CloMP_AutoBuild_input_ed.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 Refinement strategy: ['individual_sites', 'individual_adp', 'occupancies'] No refinement carried out (may need free R flags) Error message from phenix.refine: Refinement failed... Sorry: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_CloMP_AutoBuild_input_ed.pdb with aniso_refinement_data_PHX.mtz failed...quitting... /home/miket/projects/CloMP/Oxidized/APSoct2012/CloMP-TMAOcryo_B2_3/MRwithChainsAB/RefineCChalf/AutobuildPrep/AutoBuild_run_2_/LAST.LOG may have additional information... ******************************************************************************** I also checked the LAST.LOG file that is referenced in the error message. That appears to be a phenix.refine logfile, however it just cuts off after the "refinement start" header, with no information about the cause of the failure (no error message). My input MTZ file does indeed contain R-free flags. I have used this MTZ for refinement with phenix.refine (outside of autobuild) with no problems. Furthermore, earlier in the autobuild logfile, I see: Copying refinement_PHX.mtz to exptl_fobs_phases_freeR_flags.mtz Columns used: FP=FP SIGFP=SIGFP FreeR_flag=FreeRflag Which seems to me like it is recognizing my R-free flags column in the input MTZ. Does anyone have any idea what might be going wrong here?? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Phenix.refine suddenly stopped to refine B-factors
by krimmer＠staff.uni-marburg.de 12 Aug '13

12 Aug '13

Dear all, Phenix.refine suddenly stopped to refine B-factors, even though according to the settings it should refine them (checked box “individual B-factors”). This problem only occurs for one job. The weird thing is that this was always working and I did not do anything different, at least as far as I know. Also, this just happened to a colleague, totally independent from me. We never had this problem before. Here is a part of my log file: |-----overall-----|---macromolecule----|------solvent-------| stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave 0 : 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 1_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 2_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 3_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 4_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_xyz: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_adp: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_occ: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_bss: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 5_ohs: 46.46 5.37 12.45 29.68 5.37 10.14 46.46 5.58 25.33 The values are not changing at all. The structure is almost done, but it still should change a bit during the refinement cycles. I noticed the problem because I added another water molecule to the structure, and the B-factor stayed at 30.00 which resulted in a negative density blob after refinement. Thank you for your help! Stefan

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How to correct translational psuedosymmetry
by Appu kumar 12 Aug '13

12 Aug '13

Dear all, I have processed a protein-DNA complex data with imosflm. Phenix.xtriage suggest that the is a off origin peak of hight 41.702 hight at fractional coordiantes of 0.500 0.021 0.500 with distance of 40.019 from origin. I am new to such kind of problem, so would you please suggest me how to solve the psuedosymmetry problem encountered in data process. The present unit cells are 55.41 109.72 66.61 90 98.74 90 in space group P1211 with p_value is 3.116e-04. Your help would be much appreciated Thank you Appu

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is phenix trying to polymerize b-octyl glucoside?
by Edward A. Berry 09 Aug '13

09 Aug '13

I'm refining a model with some molecules of the detergent b-octyl glucoside (BOG). I got BOG.cif from a recent ccp4 library, so not sure if this is a suggestion for phenix or ccp4, but: If two BOG molecules are consecutive in the pdb file, phenix stops in setup because it can't find atom HO1 to delete. Even if I had H's in my model there would be no HO1 because O1 is in glycosidic linkage with the octyl chain. I'm guessing phenix somehow realizes there is a sugar and when two are consecutive it autogenerates a link to make a glycosidic bond between them - not appropriate in the case of BOG. easy work around is to intersperse with non-sugar molecules, but if there is a better way, I'll take it. ed RuntimeError: delete_atom_in_place: unknown atom_id: HO1 apply_mod failure: pdbres="BOG R 18 " segid="R " comp id: BOG mod id: DEL-O1 Version: dev Release tag: 1420 Platform: intel-linux-2.6-x86_64 linux

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Ensemble refinement?
by Joseph Noel 09 Aug '13

09 Aug '13

Is anyone having issues executing ensemble refinement in Phenix? I've tried several times now to run things and it always crashes without returning any maps and just returning a set of large PDB files such as: "TEAS-W273E-FPP-A_ensemble_0.6.pdb, TEAS-W273E-FPP-A_ensemble_0.8.pdb, TEAS-W273E-FPP-A_ensemble_0.9.pdb and TEAS-W273E-FPP-A_ensemble_0.1.pdb". The log file always ends with: " Time building chain proxies: 3.01, per 1000 atoms: 0.35 Number of scatterers: 8638 At special positions: 0 Unit cell: (125.75, 125.75, 120.07, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 19 16.00 P 2 15.00 Mg2+ 3 10.00 O 835 8.00 N 717 7.00 C 2765 6.00 H 4297 1.00 sf(0) = scattering factor at diffraction angle 0. AttributeError" I only entering a single chain with solvent and ions and hydrogens. All of the other parameters from the GUI are kept the same. Any suggestions or comments would be much appreciated. Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Restraints file for a modified peptide
by Michael Feldkamp 06 Aug '13

06 Aug '13

I have a peptide that has a fluorescent tag attached to its N-terminus along with a unnatural amino acid incorporated into the sequence. I know how to generate .cif files for the individual ligands using elbow, but I'm at a loss as to get Phenix to recognize these modifications to the peptide so that it refines the structure as one molecule with covalent linkages between the fluorescent tag, peptide and modified amino acid. Any help would be much appreciated. Thanks, Michael

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MR Rosetta Error
by Masaki UNNO 05 Aug '13

05 Aug '13

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: unno19(a)mx.ibaraki.ac.jp HP: http://www.fas.ibaraki.ac.jp/?page_id=961 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Molecular replacement pipeline MRage
by Morten Grøftehauge 05 Aug '13

05 Aug '13

Hi guys, So I've been trying out MRage. I used the GUI since I didn't care too much and just wanted it started. I noticed two things. It doesn't show you the best results so far. It doesn't even save the best results so far. Everything is hidden in a giant log file in the .phenix/project_data folder (.phenix is hidden so I'm guessing that means you don't want people snooping around in there?). I can grep the TFZ= lines with grep 'TFZ=' mr_pipeline.log > grep-TFZ.txtand sort them with sort -r -k 13 grep-TFZ.txt but I think this is a bit excessive for the average user. ... Oh, and now I tried to re-run the highest scoring model in Phaser and it crashed and took MRage with it. Are you sure MRage is out of beta? Trying to be facetious, not mean. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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How does phenix handle deuterium atoms in neutron diffraction data?
by Javier Gonzalez 02 Aug '13

02 Aug '13

Hello, I'm performing a joint neutron-xray refinement with phenix, for a dataset collected from a crystal exchanged with deuterated water, ie, all exchangeable H atoms are replaced by D. I was wondering whether phenix has libraries of .cif dictionaries (or equivalent) in order to handle the name "D" of some "H" atoms in the .pdb files? I would like to use those dictionaries to input into Coot, so that it can handle deuterated molecules during geometry regularization, real space refinement, etc. Any help will be greatly appreciated. Thanks, Javier -- Javier M. Gonzalez Protein Crystallography Station Bioscience Division Los Alamos National Laboratory TA-3, Building 4200, Room 202 Mailstop T001 work: (505) 667-9376 (temporary)

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feature enhanced maps
by Osman Asghar Mirza 02 Aug '13

02 Aug '13

Dear all i just installed phenix-1.8.2-1309 (OSX) and was looking for the "phenix.development.fem" but haven't been able to find it. any ideas? best osman Osman Mirza, Associate Professor PhD Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Universitetsparken 2, DK-2100 Denmark Phone: +45 3533 6175 Fax: +45 3533 6040 E-mail: om(a)farma.ku.dk<mailto:[email protected]>

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feature enhanced maps
by Osman Asghar Mirza 02 Aug '13

02 Aug '13

Dear all i just installed phenix-1.8.2-1309 (OSX) and was looking for the "phenix.development.fem" but haven't been able to find it. any ideas? best osman Osman Mirza, Associate Professor PhD Department of Drug Design and Pharmacology Faculty of Health and Medical Sciences University of Copenhagen Universitetsparken 2, DK-2100 Denmark Phone: +45 3533 6175 Fax: +45 3533 6040 E-mail: om(a)farma.ku.dk<mailto:[email protected]>

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July 2013 Computational Crystallography Newsletter
by Nigel Moriarty 01 Aug '13

01 Aug '13

Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles *cctbx* tools for transparent parallel job execution in Python. III. Remote access *phenix.ensemble_refinement*: a test study of apo and holo BACE1 Short Communications *CaBLAM*: Identification and scoring of disguised secondary structure at low resolution Structural Classification of Allergen IgE Epitopes by Hierarchical Clustering New Tool: *phenix.real_space_refine * Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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fix Ramachandran outliers
by Wei Shi 01 Aug '13

01 Aug '13

Hi all, I have a refined structure with phenix. The resolution=3.2 Å. After refinement, the R-work=0.2186, R-free=0.2864, Bonds=0.010, Angles=1.515. Ramachandran outliers: 4.8%, Ramachandran favored: 80.8%. Rotamer outliers: 14.5%, c-beta outliers: 2 clashscore: 16.28, overall score: 3.32 To fix the Ramanchandran outliers, in coot, by changing the phi-psi of the outliers, I could manage to move most of them to the allowed positions. But, after another refinement in phenix, those outliers come back. I am wondering whether any of you have any suggestions for me on how to fix these outliers. Also, I read in a previous post that “all outliers could be first fixed manually in Coot (also applying real-space refinement with Coot's Ramachandran restraints turned on), as the default potential is very tight and can pull residues the wrong way if they're starting from a very bad position”. I am wondering whether any of you have done this before in coot, and can you please tell me specifically how this is done. Thank you so much! Best, Wei

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phenix-refine crash
by Carlos Frazao 31 Jul '13

31 Jul '13

Hi, After the last model building of my protein I am not succeeding to further refine its structure, because phenix.refine crashes. However, if I set "main.number_of_macro_cycles=0" the job reaches its expected end and outputs a .pdb file. If I set "main.number_of_macro_cycles=1" the job crashes a few lines after the log-file indication " ============================== Exporting results ==============================" and produces an incomplete .pdb file with part of the header. Alternatively, If I set "main.number_of_macro_cycles=2" the job crashes during "MACRO_CYCLE 2 OF 2" after log-file indication " ----------Correcting NCS rotamer outliers---------- Set U 69 GLU to tp10 rotamer" followed by the error message : "Traceback (most recent call last): File "/usr/local/phenix/phenix-dev-1391/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/command_line.py", line 161, in run call_back_handler=call_back_handler) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/driver.py", line 1659, in run ncs_manager = self.ncs_manager).result File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/strategies.py", line 170, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", line 66, in __init__ self.call(self.ncsrot, "NCS rotamer correction") File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", line 101, in call func(prefix = prefix) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", line 146, in ncsrot log = self.log) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/misc.py", line 89, in ncs_rotamer_update log=log) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", line 1111, in fix_rotamer_outliers key=key) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/rotamer_search.py", line 178, in search assert rotamer == cur_rotamer AssertionError" I have been using built phenix-dev-1391 (I also checked phenix version 1.8.2-1309 or built dev-1436, they crashed as well) x86_64-fc3, in a machine running Ubuntu 10.04.4 LTS with Python 2.6.5. I tried another machine, running Ubuntu 12.04 LTS with Python 2.7.3, and using built phenix-dev-1391 x86_64-fc3 I got at the end of the log-file: " ----------Correcting NCS rotamer outliers---------- Traceback (most recent call last): File "/usr/local/phenix/phenix-dev-1391/build/intel-linux-2.6/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/command_line.py", line 161, in run call_back_handler=call_back_handler) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/driver.py", line 1659, in run ncs_manager = self.ncs_manager).result File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/strategies.py", line 170, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", line 66, in __init__ self.call(self.ncsrot, "NCS rotamer correction") File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", line 101, in call func(prefix = prefix) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", line 146, in ncsrot log = self.log) File "/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/misc.py", line 89, in ncs_rotamer_update log=log) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", line 1044, in fix_rotamer_outliers self.rotamer_search_manager.prepare_map(fmodel=fmodel) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/rotamer_search.py", line 57, in prepare_map torsion_utils.prepare_map(fmodel=fmodel) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/utils.py", line 771, in prepare_map not exclude_free_r_reflections)) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/map_tools.py", line 242, in fft_map symmetry_flags = symmetry_flags) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/cctbx/miller/__init__.py", line 3420, in fft_map f_000=f_000) File "/usr/local/phenix/phenix-dev-1391/cctbx_project/cctbx/miller/__init__.py", line 4236, in __init__ conjugate_flag=True) MemoryError"- I did not succeed to find out what may I have done wrong with the model and/or params files Any help is highly appreciated, Carlos -- ************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, P Phone: (351)-214469666 FAX: (351)-214433644 e-mail: frazao(a)itqb.unl.pt www.itqb.unl.pt

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distance threshold for special positions?
by Alastair Fyfe 31 Jul '13

31 Jul '13

I'd be grateful for pointers to documentation/source regarding phenix.refine's criterion for flagging an atom's coordinates as coinciding with a special position. For shelxl I noticed a distance cutoff of 0.02 to the symmetry equivalent position seems adequate for the data I'm working with. For phenix.refine the threshold is higher but I haven't found documentation for the cutoff used. thanks, Alastair Fyfe

2 1

proteins sequence for phenix
by LISA 26 Jul '13

26 Jul '13

Dear All, Phenix will ask for the protein sequence when we create a new project. I try to solve my complex by the Autosol in phenix with proteins sequence. My complex contains 2 molecule A and 3 molecule B. How can I give the sequence in phenix? will it should be: >A .................................................................................................................. >B .............................................................................................................................. or >A .................................................................................................................. >A .................................................................................................................. >B .............................................................................................................................. >B .............................................................................................................................. >B .............................................................................................................................. Thank you. Lisa

3 2

Re: [phenixbb] On Mac two separate installations?
by Joseph Noel 26 Jul '13

26 Jul '13

Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Also, following the protocol as outlined by Andy Karplus in his Science paper on data processing using data extending to CC1/2's near 0.2. Both together seem to really extend the resolution of my datasets and also improve refinement! ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Fwd: Course on “Structure and Function of Membrane Proteins- a multidisciplinary approach”
by Nathaniel Echols 26 Jul '13

26 Jul '13

---------- Forwarded message ---------- From: Jose Artur Brito <jbrito(a)itqb.unl.pt> To: phenixbb(a)phenix-online.org Date: Fri, 26 Jul 2013 15:58:01 +0100 Subject: Course on “Structure and Function of Membrane Proteins- a multidisciplinary approach” Dear colleagues, We would like to announce the Instruct-sponsored 4-day course “Structure and Function of Membrane Proteins- a multidisciplinary approach”, to be held at ITQB, Oeiras (nearby Lisbon), Portugal, from 5 to 8 November 2013. The course will address several techniques for the structural and functional characterization of membrane proteins, with special emphasis on Macromolecular Crystallography, Mass Spectrometry, Electron Microscopy and Nuclear Magnetic Ressonance. The information provided by each technique, their applications in biological systems, major benefits and limitations will be discussed. The course is organized with lectures in the mornings and interactive tutorials in the afternoons. In addition, the selected applicants are grouped and each group works on a case study (based on 2-3 papers covering techniques of interest and a questionnaire) and gives a presentation at the end of the course. The course is aimed primarily at PhD students, young Post-Doctoral researchers and others with research activities involving structural biology of membrane proteins. Participants will be limited to 20. Candidate selection will be based on a short CV, a motivation letter from the applicant, and a recommendation letter from the supervisor. Registration deadline is September 16, please send your application to membstruct2013(a)itqb.unl.pt . More information can be found at http://www.itqb.unl.pt/membstruct2013 The organizing commission, Margarida Archer (ITQB-UNL), Carlos Cordeiro (FC-UL) and José A. Brito (ITQB-UNL) -- ************************************************ * José Artur Brito, PhD * * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal * * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbrito(a)itqb.unl.pt * * URL: http://mx.itqb.unl.pt * ************************************************

1 0

Linux distribution question: who needs the FC3 build?
by Nathaniel Echols 25 Jul '13

25 Jul '13

Dear users, We are in the process of rearranging our server room and changing the way we do the nightly builds. One step of this will be retiring the bulky and ancient boxes which run Fedora 3, and standardizing on slightly more modern OSes. (Including Ubuntu-specific builds, as well as the usual Fedora/RedHat/CentOS base.) I know that some people have found that the Fedora 8 x86_64 build does *not* run properly on their systems, but the Fedora 3 build does. Could anyone who has firsthand experience with this please contact me off-list and tell me exactly which distribution and version you are running? We can't cover all possible combinations (sorry Gentoo users), but I'd like to get some idea what is still problematic. thanks, Nat

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Refinement using a homolog as a reference
by Joshi, Amar (Dr.) 25 Jul '13

25 Jul '13

Hi, I am refining ligand-protein complexes at 3.2Å dataset with a human protein. My Rfree is ~0.34 but my ramachandran stats are concerning me: 85% favoured, 4.5% disallowed. The structure of a yeast homolog has been deposited at 2.4Å resolution. The yeast structure contains additional loops but is ~55% identical to the human protein. The overall conformation between the homologs is very similar. Can I use this as a reference model? Should I prune the reference model? Will different numbering schemes affect the refinement? Many thanks, Amar

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Re: [phenixbb] Linux distribution question: who needs the FC3 build?
by Nathaniel Echols 25 Jul '13

25 Jul '13

On Wed, Jul 24, 2013 at 2:56 PM, Edward A. Berry <BerryE(a)upstate.edu> wrote: > Would that be the end of support for 32-bit linux? Or would you build > i686 version on a later version? (Or is it possible to run 64 bit > executable on 32- bit operating systems with some kind of compatibility > libraries and 64-bit capable hardware?) > > I have one Fc8 32 bit machine which I don't want to upgrade, but I don't > really need to run phenix on it. Just to clarify: we will continue distributing 32-bit Linux indefinitely (although probably on fewer platforms than 64-bit), and we will at least support Fedora 8 at a minimum for a while, since our most important development system is still running it. The question is really related to how ancient a distribution we need to support, and what scenarios are especially difficult for binary cross-compatibility. -Nat

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calculate map from ensemble refinement
by Bard, Joel 23 Jul '13

23 Jul '13

Hi- I ran phenix.ensemble refinement which worked very nicely but crashed during map output. I think this was my fault for using a parameter file that had map_type = None (I didn't look and assumed the default was reasonable). I would like to calculate maps after the fact. Is there a way to run the map calculation on the output ensemble pdb file and reflection data? I tried phenix.maps which choked on the huge ensemble. Thanks, Joel

3 3

Group ADP refinement
by joseph Lyons 23 Jul '13

23 Jul '13

Dear phenixbb. I am currently running phenix 1.8.2-1309. My goal is to use group ADP with 2 b-factors per residue for the protein and individual b-factors for solvent. However, this does not seem to be working even though the system seems to recognise what I want to do. The refinement output gives what looks like individual b-factor refinement... ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4048 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 127 aniso = 0) group_adp = True (3921 atoms in 967 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False In troubleshooting it appears that with Group ADP with 2 b-factors per residue, the solvent B-factors are not being refined, i.e., remaining at the Wilson B that I set previously. For Group ADP with 1 b-factors per residue - everything appears to refine OK. Any help would be greatly appreciated, Regards, Joe

2 1

Re: [phenixbb] How do I turn off sidechain rotamer fitting? (Pavel Afonine)
by Joseph Noel 23 Jul '13

23 Jul '13

Dear Pavel, To clarify, in the latest nightly build, 1435, do you have to click on real space refinement to carry out side chain rotamer fitting? If you just refine xyz I assume side chain rotamer fitting is not enabled, correct? Joe Noel ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Re: [phenixbb] Phenix "hangs" on a Mac?
by Joseph Noel 23 Jul '13

23 Jul '13

Hi Nat, Will replicate and send you the information. Its unrelated to Ramachandran restraints as it occurs intermittantly when doing just regular tasks. I can always tell early as it never seems to get past the first steps of the refinement protocol - in essence - it never starts xyz refinement. Just sits there. I abort and restart and it then goes fine. I'm running Mac OSX 10.8.4 Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

1 0

Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Jul '13

23 Jul '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E as well as who to contact for more information. Information about the MAX IV laboratory can be obtained at www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Phenix "hangs" on a Mac?
by Joseph Noel 22 Jul '13

22 Jul '13

Has anyone had a problem when using Phenix refine through the GUI on a Mac wherein the program after hitting Run locally starts but then hangs without proceeding? Seems to happen to me about one out of five times I run refine and always hangs when I experiment with ramachandran restraints for only a portion of the polypeptide chain. I've tried letting things alone for several hours and nothing happens. I can abort and then often resubmit and it then runs fine (except for rama restraints). I've found this happens with both nightly builds and stable releases. I am currently running the latest nightly build 1439. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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On Mac two separate installations?
by Joseph Noel 22 Jul '13

22 Jul '13

Does one have to install both the GUI and command line installers on a Mac if one wants to have the option of running using the command line (for command line only options in nightly builds) and the GUI? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

2 1

mr_rosetta pause & resume
by Karolina Michalska 22 Jul '13

22 Jul '13

Hello everybody, Is there a way to pause an mr_rosetta run and resume it with a different number of processors? Thanks, Karolina

3 3

Registration open: "The Future of Microfocus Protein Crystallography"
by Marjolein Thunnissen 22 Jul '13

22 Jul '13

Dear all, I would like to remind you on a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White, Luca Jovine and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting, but there is no requirement to be a user of the facility and all that are interested are welcome . Registration is through the user meeting website: https://indico.maxlab.lu.se/indico/conferenceDisplay.py?confId=0 . The registration fees are 2000 SEK for academics and 700 SEK for junior scientists. Registration fees include all lunches and the conference dinner. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

1 0

Fo-Fo map
by Xiang Li 22 Jul '13

22 Jul '13

Hi everyone, I am working on two datasets of the similar crystal design. In one of the datasets, there is an extra guest protein (might be considered as a ligand) docked in one unit cell. The two crystals have very similar unit cell size and same symmetry. I want to calculate the Fo-Fo map to see whether I could figure out where the protein is. But I got error says the symmetry of the two datasets are not the same. I have never used the "isomorphous difference map" in GUI before. Can anyone help me to figure out where I did wrong please? I have attached the mtz file that I want to compare. Btw, if the protein is not very rigidly linked with the crystal framework (~2 free residues linkage), am I supposed to see the density of the protein? Or are there any better ways for me to identify the protein? Thanks for your kind help! Sincerely, Xiang

2 2

ADP refinement of cysteinesulfonic acid
by Phillip Steindel 16 Jul '13

16 Jul '13

Hi all- I have a 1.5 Angstrom structure with two cysteines that appear to have oxidized to cysteinesulfonic acid (OCS). I replaced the cysteines in coot, then ran refine with individual and anisotropic ADPs, but the ADPs don't appear to be refining for those residues. The hydrogens are all at 24,and the non-hydrogens are all at 20. I'm running 1.8.2-1309. Thanks, Phillip Steindel Theobald Lab Brandeis University

2 1

cis peptide question
by Edward A. Berry 16 Jul '13

16 Jul '13

I have a cis-peptide in my structure. Phenix recognizes it and .geo file shows this is restrained to 0*: dihedral pdb=" CA ALA A 401 " pdb=" C ALA A 401 " pdb=" N SER A 402 " pdb=" CA SER A 402 " ideal model delta harmonic sigma weight residual 0.00 -1.58 1.58 0 5.00e+00 4.00e-02 1.00e-01 However in statistics printed with the output pdb, I have at least one dihedral that is flagged as off by about 180*: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 DIHEDRAL : 12.902 168.987 3277 ^^^^^^^ Could this be my cis peptide, or do I have a really bad dihedral somewhere else?

3 4

How do I turn off sidechain rotamer fitting?
by Owen Pornillos 15 Jul '13

15 Jul '13

I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature? Many thanks, Owen

2 4

Kicked difference maps
by Ho Leung Ng 13 Jul '13

13 Jul '13

Hi, I am finding that features in kicked difference maps (mFo-DFc) have very different scaling compared to the standard difference maps. For example, a blob that appears in the standard map at 3 sigma might not appear in the kicked map until 5.5 sigma. Is this correct functioning? In contrast, features in the kicked and standard 2mFo-DFc maps are comparable in scale. Thank you, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry hng(a)hawaii.edu

2 1

problem with alternate conformations
by George Phillips 11 Jul '13

11 Jul '13

I am trying to adapt my old CNS scripts to to multiple conformer refinements in Phenix, i.e. up to 20 copies of each entire chain. I seem to be OK with up to three copies of the whole chain, but when I try four or more I seem to be in an infinite loop in the 'reduce' phase of a refinement. 3 copies runs in less than hour, even with torsion simulated annealing, with four even overnight the program just runs 'reduce for hours and hours'. This happens on the standard release and development version 1422. Is there some way to turn off hydrogens as a work around? Test files available on request. : ) Thanks for any help! George George N. Phillips, Jr. Ralph and Dorothy Looney Professor Department of Biochemistry and Cell Biology Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 http://www.bioc.rice.edu/

3 5

2014 Gordon Research Conference and Research Seminars on Diffraction Methods in Structural Biology
by Anastassis Perrakis 11 Jul '13

11 Jul '13

Dear all, In a bit more than a year from now, we will be running the Gordon Research Conference on Diffraction Methods in Structural Biology, this time preceded for the first time by a two-day Gordon Research Seminar, exclusively for young scientists and a few mentors. http://www.grc.org/programs.aspx?year=2014&program=diffrac http://www.grc.org/programs.aspx?year=2014&program=grs_diff We are in the process of inviting the right people to make the schedule as exciting and inviting as possible, hoping we will be able to attract a diverse, enthusiastic, and motivated crowd! At this stage, we would like to ask you for ideas for 1. Specific subjects that are emerging and you would like to see covered, to make it worth your time to join us! 2. Specific people that would be excellent speakers, that would make you attend the Research Conference! 3. Specific people that would be great mentors, that would make you attend the Research Seminars! Many thanks from the team (but please send all replied to me!) Tassos Perrakis (GRC chair), Eddie Snell (GRC vice chair), Jeff Headd (GRS chair) and Maike Bublitz (GRS assoc. chair)

1 0

parallel phenix.phaser on SGE cluster
by L. Costenaro (IBB) 11 Jul '13

11 Jul '13

Hello, I am trying to run phaser in a SGE cluster (qsub) using multiple proc (either phenix.phaser from the command line or phaser-MR from the GUI), but the jobs do not parallelize. When I run the phaser-MR locally (same executable) it does parallelize (multiple python threads). Any help , advice would be welcome. Best regards, Lionel

3 3

Location of Gaussian factors for ED calculation
by Schubert, Carsten [JRDUS] 10 Jul '13

10 Jul '13

Hi, Were in the phenix package can I find the Gaussian factors (scattering table) for calculating the isotropic ED distribution at a given radius of r. I just need that for an illustration. Even better of you could already point me to some plots. Nothing I found online so far was suitable. Thanks Carsten

2 2

: Post-doctoral position in structural biology (Paris, France)
by Benas Philippe 10 Jul '13

10 Jul '13

POST-DOCTORAL POSITION IN STRUCTURAL BIOLOGY (PARIS, FRANCE) . A postdoctoral position is available in the group of Dr. Carine Tisne at the Laboratory of Biological Crystallography and NMR of the University Paris Descartes, jointly with the group of Dr. Ciaran Condon at the Laboratory of Microbial Gene Expression (CNRS UPR9073) of the Institut de Biologie Physico-Chimique. We are studying the structure, function and folding of RNA and their complexes using NMR spectroscopy and X-ray crystallography, together with complementary biophysical methods. The postdoctoral research project focusses on the processing of the 5 and 3 ends of 5S rRNA in Gram-positive bacteria using solution NMR and X-ray crystallography as the main techniques. An integral part of our projects is the use and development of state-of-the-art preparative, biochemical and NMR techniques. . Interested candidates should hold a Ph.D. in Biochemistry, Biophysics or Structural Biology. Expertise in NMR spectroscopy and/or X-ray crystallography is mandatory. The successful candidate should be highly motivated, creative and capable of independent research in a two-team environment (10 minute walk between labs). The position is for a two-year term contract (one year in each team). We offer an exciting and enthusiastic work environment together with a stimulating location at the center of Paris (close to Jardin du Luxembourg). Facilities for structural biology include 600 MHz Bruker spectrometer equipped with cryoprobe. A new 700 MHz spectrometer will be installed in 2014. We also have access to high-field NMR spectrometers through the French TGIR and regular access to synchroton beamtime at either the ESRF or SOLEIL as Beam Time Allocation Group member. The ideal start date for the position would be October 2013. . Applications and informal queries about the labs and research projects should be directed by email to Carine Tisne (carine.tisne(a)parisdescartes.fr) or Ciaran Condon (condon(a)ibpc.fr[1]). Applications must include a letter of motivation summarizing current and future research interests, a CV, list of publications and letters of recommendation from at least two references. . ------------------------- PHILIPPE BENAS, PH.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.benas(a)parisdescartes.fr, philippe_benas(a)yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 ------------------------- "We do know nothing ! But tomorrow is another day ! ;-) " Liens: ------ [1] mailto:[email protected]

1 0

give-up-quick Phaser in Rosetta
by Morten Grøftehauge 10 Jul '13

10 Jul '13

Dear Phenixbb, I was wondering if there was any way of getting Rosetta to give up easily and move on to another search model? Say I have 20 or more equally awful search models. I think there's a possibility that one of them will knock it out of the park (i.e. TFZ > 8). But even if I have Phaser set to fast search I will end up with an exhaustive search because the search models are so bad. fast_search_mode= True Run phaser with selection_criteria_rot_value and then if no obvious solution, repeat with cutoff lowered by search_down_percent search_down_percent= 25 Used if fast_search_mode=True. Run phaser with selection_criteria_rot_value and then if no obvious solution, repeat with cutoff lowered by search_down_percent If I set search_down_percent to 75 does this mean that Phaser will give up easily and move on to the next model? Is this a terrible strategy CPU-time-wise? I am of course aware that search_down_percent is much more likely to give me the right solution for a given model but in this case there are just so many possible search models. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

2 2

inconsistent Rwork/Rfree in outputs
by Michael Thompson 09 Jul '13

09 Jul '13

Hello All, I am getting an output from phenix.refine that is somewhat confusing to me. I have a log file that seems to be reporting inconsistent values for the final Rwork and Rfree. The last line of my log file says: Final R-work = 0.1815, R-free = 0.1912 However, when I check the pdb file from phenix.refine, I see: REMARK Final: r_work = 0.1799 r_free = 0.1952 bonds = 0.012 angles = 1.315 In the log file, I get the following table, which seems to agree with what is in the pdb file. R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.1971 0.1916 1.408780e-01 1.965297e-01 1_bss: 0.1971 0.1916 1.508155e-01 2.122150e-01 1_ohs: 0.1971 0.1916 1.447084e-01 2.026856e-01 1_xyz: 0.1928 0.2001 1.348543e-01 2.162596e-01 1_adp: 0.1929 0.2134 1.006068e-01 1.652532e-01 1_occ: 0.1928 0.2127 9.708801e-02 1.642701e-01 2_bss: 0.1784 0.1978 1.001979e-01 1.536656e-01 2_ohs: 0.1786 0.1982 1.146147e-01 1.876601e-01 2_xyz: 0.1777 0.1959 1.187570e-01 1.899659e-01 2_adp: 0.1952 0.2001 1.109064e-01 1.588435e-01 2_occ: 0.1952 0.1995 1.059382e-01 1.580417e-01 3_bss: 0.1831 0.1888 1.066004e-01 1.508888e-01 3_ohs: 0.1833 0.1890 1.217008e-01 1.855605e-01 3_xyz: 0.1824 0.1897 1.256200e-01 1.855714e-01 3_adp: 0.1876 0.2039 1.027854e-01 1.533022e-01 3_occ: 0.1877 0.2042 9.739524e-02 1.525993e-01 4_bss: 0.1770 0.1931 9.830779e-02 1.515598e-01 4_ohs: 0.1772 0.1933 1.132096e-01 1.824877e-01 4_xyz: 0.1775 0.1933 1.179076e-01 1.860704e-01 4_adp: 0.1911 0.2005 1.074584e-01 1.546149e-01 4_occ: 0.1909 0.1997 1.023003e-01 1.530269e-01 5_bss: 0.1805 0.1895 1.034638e-01 1.506407e-01 5_ohs: 0.1807 0.1895 1.185810e-01 1.828381e-01 5_xyz: 0.1803 0.1899 1.244219e-01 1.801964e-01 5_adp: 0.1893 0.2019 1.072974e-01 1.503622e-01 5_occ: 0.1893 0.2023 1.016701e-01 1.492730e-01 6_bss: 0.1792 0.1915 1.021896e-01 1.490341e-01 6_ohs: 0.1794 0.1915 1.174694e-01 1.798680e-01 6_xyz: 0.1804 0.1926 1.224254e-01 1.830383e-01 6_adp: 0.1952 0.2015 1.118187e-01 1.549205e-01 6_occ: 0.1950 0.2017 1.063759e-01 1.538692e-01 7_bss: 0.1842 0.1922 1.076805e-01 1.529198e-01 7_ohs: 0.1845 0.1918 1.227818e-01 1.857086e-01 7_xyz: 0.1846 0.1917 1.292627e-01 1.856928e-01 7_adp: 0.1885 0.2042 1.071531e-01 1.532154e-01 7_occ: 0.1885 0.2044 1.012764e-01 1.524448e-01 7_bss: 0.1797 0.1952 1.353649e-01 1.556126e-01 7_ohs: 0.1799 0.1952 1.353649e-01 1.556126e-01 I'm wondering why this last line of the log file isn't consistent with the other values that are being reported for R/Rfree? Which numbers should I believe? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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GUI admin issues
by Yarrow Madrona 09 Jul '13

09 Jul '13

Hello, I have a couple of GUI related questions 1. We recently moved all of our data from one hard drive to another. However, we do not know how to change the directory for all of our projects. The directory is similar but the hard drive is now called tp3home instead of tp2home. We found a .phenix directory that has a file with a list of projects and directories. We updated the directories but this did not make a difference in the GUI. 2. Is there a quick way to specify which ligand or amino acid to remove in the GUI with doing simmulated annealing or better to do manually? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] omit map for protein-DNA complex
by Wei Shi 09 Jul '13

09 Jul '13

Hi guys, With the help of Tom and Nat, I fixed the errors in my pdb file and could generate the simulated annealing omit map for the protein-DNA complex structure! But when I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I could only see one monomer of the protein in Coot. It should be two dimers of the protein plus two pieces of DNA. And when I opened the *_ed.pdb in pymol, it showed the right thing: two dimers of the protein plus two pieces of DNA. It seems that something in *_ed.pdb file is not recognized by Coot. I don't know whether any of you had this before and would have any suggestions for me. When I opened *_ed. pdb with text file and found out that the word "break" is used instead of "ter" between different chains, so I replaced all "break" with "ter", but this didn't help.... Thank you so much! Best, Wei On Wed, Jul 3, 2013 at 10:36 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: > Hi Nat and Tom, > Thank you so much for your help! I don't know why those C7 atoms are > there.... I just added some nucleotides manually using coot to fit the > density. I am going to delete those C7 atoms in DA and see whether that > would help. Thank you guys so much! > > Best, > Wei > > On Tue, Jul 2, 2013 at 5:22 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > >> Okay, this makes sense. Wei, are you trying to model methylated DNA, >> or are those C7 atoms there by accident? >> >> -Nat >> >> On Tue, Jul 2, 2013 at 12:11 PM, Terwilliger, Thomas C >> <terwilliger(a)lanl.gov> wrote: >> > Hi Nat, >> > I think it was the input file. Here is a little piece of it: >> > >> > ATOM 3157 P DA E 8 -56.682 44.723-118.292 1.00 37.45 >> P >> > ATOM 3158 C5' DA E 8 -54.313 44.743-117.204 1.00 40.32 >> C >> > ATOM 3159 O5' DA E 8 -55.729 44.807-117.015 1.00 38.38 >> O >> > ATOM 3160 C4' DA E 8 -53.551 44.795-115.886 1.00 35.58 >> C >> > ATOM 3161 O4' DA E 8 -53.433 46.172-115.429 1.00 32.68 >> O >> > ATOM 3162 C3' DA E 8 -54.164 44.027-114.709 1.00 30.30 >> C >> > ATOM 3163 O3' DA E 8 -53.117 43.597-113.848 1.00 30.92 >> O >> > ATOM 3164 C2' DA E 8 -54.997 45.106-114.029 1.00 18.46 >> C >> > ATOM 3165 C1' DA E 8 -53.974 46.233-114.120 1.00 19.87 >> C >> > ATOM 3166 N1 DA E 8 -52.933 50.956-112.506 1.00 4.27 >> N >> > ATOM 3167 C2 DA E 8 -52.179 49.849-112.633 1.00 5.31 >> C >> > ATOM 3168 N3 DA E 8 -52.515 48.630-113.069 1.00 3.59 >> N >> > ATOM 3169 C4 DA E 8 -53.816 48.619-113.401 1.00 5.26 >> C >> > ATOM 3170 C5 DA E 8 -54.722 49.662-113.344 1.00 5.31 >> C >> > ATOM 3171 C6 DA E 8 -54.237 50.894-112.863 1.00 4.84 >> C >> > ATOM 3172 N6 DA E 8 -55.010 51.981-112.750 1.00 5.38 >> N >> > ATOM 3173 C7 DA E 8 -56.909 56.086-110.227 1.00 2.18 >> C >> > ATOM 3174 N7 DA E 8 -55.973 49.258-113.789 1.00 6.11 >> N >> > ATOM 3175 C8 DA E 8 -55.803 47.992-114.102 1.00 7.27 >> C >> > ATOM 3176 N9 DA E 8 -54.525 47.556-113.888 1.00 8.54 >> N >> > ATOM 3177 OP1 DA E 8 -56.215 43.588-119.122 1.00 44.46 >> O >> > ATOM 3178 OP2 DA E 8 -58.094 44.785-117.853 1.00 32.00 >> O >> > >> > Notice the C7 that is not attached to anything and is not normally part >> of a DA nucleotide. >> > -Tom T >> > >> > On Jul 2, 2013, at 1:07 PM, Nathaniel Echols wrote: >> > >> >> On Tue, Jul 2, 2013 at 9:03 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: >> >>> Below is the error message I got when I ran a plain refinement of the >> same >> >>> PDB file and data file. I also ran phenix.ready-set of the PDB file >> using >> >>> default setting (add hydrogen to model if absent, et al) and generate >> a >> >>> updated PDB file and ran refine again, but still got the same error >> message >> >>> as below: >> >> >> >> This sounds like a bug. Could you please email us off-list with the >> >> PDB file and any existing restraints? (We can fake the data for >> >> testing purposes.) >> >> >> >> -Nat >> > >> > >

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Re: [phenixbb] problem refining Fe-S cluster
by Edward A. Berry 05 Jul '13

05 Jul '13

Pavel Afonine wrote: > Hi Ed, > > it looks like occupancies and B-factors need to be refined and refined > until convergence. Also, if you apply any distance restraints for > clusters (restrain Fe-S distances) make sure these restraints are > correct. I've seen many cases like this and typically refining > occupancy/b-factors and making sure restraints are correct solves the > problem. I've never seen fixing specific parameters help and I can't > understand logic for doing this. > OK. I'm not giving any restraints for the cluster, it must be in the monomers library. I can get SF4.cif from CCP4 and set the weights for bonds/angles very low to let the density rule. But now I see the problem wasn't there a few rounds back, and the difference seems to be that I was using 3 macro_cyles instead of 1. Now I repeat exactly the same refinement both ways, seems to be it. So maybe an artifact of not refining to convergence. Odd though, because it was OK in the starting model, and I'm not asking for the B's to be reset initially to 20 or something. Problem seems to be solved by using the default 3 cycles, but in case anyone is interested, B-factors for Fe are pretty much unchanged after refining 3 cycles B-factors for the Fe's but not the S's, decrease by about 5.0 on refining 1 cycle. Overall and protein B-ave increase on refining 1 cycle Looking at the step by step changes, the first cycle out of 3 is not like the single cycle. This is dev-1420 version of phenix. R-factors refining 3 cycles REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3205 0.3532 3.857969e+00 3.920754e+00 REMARK 1_bss: 0.2433 0.2823 3.683390e+00 3.779722e+00 REMARK 1_weight: 0.2433 0.2823 3.683390e+00 3.779722e+00 REMARK 1_xyzrec: 0.2457 0.2825 3.689060e+00 3.780966e+00 REMARK 1_adp: 0.2463 0.2823 3.690454e+00 3.780932e+00 REMARK 1_occ: 0.2463 0.2823 3.690455e+00 3.780936e+00 REMARK 2_bss: 0.2463 0.2823 3.690087e+00 3.780536e+00 REMARK 2_weight: 0.2463 0.2823 3.690087e+00 3.780536e+00 REMARK 2_xyzrec: 0.2439 0.2821 3.684528e+00 3.778960e+00 REMARK 2_adp: 0.2434 0.2823 3.683429e+00 3.779315e+00 REMARK 2_occ: 0.2434 0.2823 3.683429e+00 3.779316e+00 REMARK 3_bss: 0.2433 0.2825 3.683615e+00 3.779760e+00 REMARK 3_weight: 0.2433 0.2825 3.683615e+00 3.779760e+00 REMARK 3_xyzrec: 0.2455 0.2825 3.688717e+00 3.780899e+00 REMARK 3_adp: 0.2461 0.2824 3.689934e+00 3.780715e+00 REMARK 3_occ: 0.2461 0.2824 3.689934e+00 3.780714e+00 REMARK end: 0.2457 0.2825 3.689963e+00 3.781089e+00 refining 1 cycle REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3205 0.3532 3.857969e+00 3.920754e+00 REMARK 1_bss: 0.2222 0.2930 3.668217e+00 3.804573e+00 REMARK 1_weight: 0.2222 0.2930 3.668217e+00 3.804573e+00 REMARK 1_xyzrec: 0.2284 0.2941 3.681902e+00 3.808504e+00 REMARK 1_adp: 0.2594 0.3133 3.748285e+00 3.841014e+00 REMARK 1_occ: 0.2594 0.3133 3.748284e+00 3.841012e+00 REMARK end: 0.2692 0.2912 3.759155e+00 3.806820e+00 REMARK ------------------------------------------------------------------------ R B-factors refining 3 cycles REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 90.34 16.23 43.10 90.34 16.23 42.91 80.33 27.29 46.57 REMARK 1_bss: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_weight: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_xyzrec: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_adp: 89.27 16.38 42.96 89.27 16.38 42.79 80.39 26.98 46.24 REMARK 1_occ: 89.27 16.38 42.96 89.27 16.38 42.79 80.39 26.98 46.24 REMARK 2_bss: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_weight: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_xyzrec: 89.37 16.47 43.06 89.37 16.47 42.88 80.49 27.08 46.34 REMARK 2_adp: 89.46 16.19 42.92 89.46 16.19 42.74 80.48 26.86 46.22 REMARK 2_occ: 89.46 16.19 42.92 89.46 16.19 42.74 80.48 26.86 46.22 REMARK 3_bss: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_weight: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_xyzrec: 89.63 16.36 43.09 89.63 16.36 42.92 80.66 27.03 46.39 REMARK 3_adp: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 REMARK 3_occ: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 REMARK end: 89.22 16.53 42.92 89.22 16.53 42.75 80.45 26.77 46.08 refining 1 cycle: REMARK |-----overall-----|---macromolecule----|------solvent-------| REMARK stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave REMARK 0 : 90.34 16.23 43.10 90.34 16.23 42.91 80.33 27.29 46.57 REMARK 1_bss: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_weight: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_xyzrec: 90.40 16.29 43.15 90.40 16.29 42.97 80.39 27.35 46.63 REMARK 1_adp: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK 1_occ: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK end: 85.40 23.38 49.20 85.40 23.38 49.17 81.25 33.88 49.84 REMARK ------------------------------------------------------------------------ R starting model oswego 236% grep SF4 sqr1402e_002.pdb ATOM 8568 FE4 SF4 B1003 15.699 21.265 101.440 1.00 31.53 Fe ATOM 8569 FE1 SF4 B1003 15.302 20.444 104.268 1.00 28.32 Fe ATOM 8570 FE3 SF4 B1003 15.072 18.385 101.975 1.00 30.57 Fe ATOM 8571 FE2 SF4 B1003 17.702 19.420 102.964 1.00 32.57 Fe ATOM 8572 S2 SF4 B1003 14.066 20.264 102.463 1.00 39.50 S ATOM 8573 S3 SF4 B1003 16.963 21.440 103.248 1.00 28.46 S ATOM 8574 S1 SF4 B1003 16.723 19.393 100.994 1.00 31.08 S ATOM 8575 S4 SF4 B1003 16.026 18.425 103.963 1.00 29.56 S refining 3 cycles oswego 235% grep SF4 sqr1402e_006.pdb ATOM 8568 FE4 SF4 B1003 15.708 21.268 101.432 1.00 31.37 Fe ATOM 8569 FE1 SF4 B1003 15.283 20.449 104.291 1.00 28.14 Fe ATOM 8570 FE3 SF4 B1003 15.062 18.373 101.986 1.00 30.15 Fe ATOM 8571 FE2 SF4 B1003 17.720 19.419 102.961 1.00 32.34 Fe ATOM 8572 S2 SF4 B1003 14.080 20.264 102.462 1.00 38.64 S ATOM 8573 S3 SF4 B1003 16.943 21.422 103.257 1.00 28.96 S ATOM 8574 S1 SF4 B1003 16.712 19.383 101.004 1.00 31.27 S ATOM 8575 S4 SF4 B1003 16.036 18.446 103.959 1.00 29.32 S refining 1 cycle oswego 234% grep SF4 sqr1402e_005.pdb ATOM 8568 FE4 SF4 B1003 15.763 21.282 101.383 1.00 26.59 Fe ATOM 8569 FE1 SF4 B1003 15.274 20.434 104.305 1.00 23.38 Fe ATOM 8570 FE3 SF4 B1003 15.026 18.351 102.006 1.00 25.63 Fe ATOM 8571 FE2 SF4 B1003 17.779 19.437 102.902 1.00 27.63 Fe ATOM 8572 S2 SF4 B1003 14.132 20.305 102.437 1.00 34.56 S ATOM 8573 S3 SF4 B1003 16.929 21.408 103.255 1.00 28.42 S ATOM 8574 S1 SF4 B1003 16.681 19.335 101.002 1.00 29.49 S ATOM 8575 S4 SF4 B1003 16.105 18.462 103.923 1.00 28.25 S

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problem refining Fe-S cluster
by Edward A. Berry 05 Jul '13

05 Jul '13

I have a problem refining a structure with iron-sulfur clusters. The irons refine to low B-factors (~25 in this case, while wilson B and B-average are around 45 and the Sg's ligating the irons are ~30). The irons have negative difference density and there is positive density in the center of the cluster (not on the S as it appears; the S is actually above the plane of the irons and the positive density below). (see attached map) It's possible that the cluster is lost in some percent of the molecules, and I could refine occupancy to get rid of the negative density, but I suspect this is likely to be because the B-factors are too low. I will try manually setting B for the Fe's and refining without ADP step, but does anyone have a better suggestion? This was refined for one macrocycle with strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous thanks, eab

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divergence of R and Rfree at the last step of refinement
by Edward A. Berry 04 Jul '13

04 Jul '13

I'm refining a structure with phenix-dev-1414 version, and R-free decreases until the last step where R-work drops sharply and R-free increases. Am I doing something wrong? R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3068 0.3347 4.111964e+00 4.184576e+00 1_bss: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_weight: 0.2296 0.2735 3.919523e+00 4.036648e+00 1_xyzrec: 0.2377 0.2725 3.938818e+00 4.036514e+00 1_adp: 0.2311 0.2707 3.918953e+00 4.031556e+00 1_occ: 0.2311 0.2707 3.918944e+00 4.031541e+00 end: 0.2187 0.2795 3.907777e+00 4.050961e+00 ////////////////////////////////////////////////////////////////// Looking in the log file, it seems that this happens at the stage of correcting the solvent mask: ============================= updating all scales ============================= start: r_work=0.3152 r_free=0.3389 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2324 r_free=0.2703 remove outliers: r_work=0.2324 r_free=0.2703 *-> correct solvent mask: r_work=0.2187 r_free=0.2795 <--*** final: r_work=0.2187 r_free=0.2795 overall anisotropic scale matrix: V0: 2.5130,-0.3626,1.3424,-0.7174,-0.0625,-2.3276 V1: -0.0348,-0.0556,-0.0105,-0.0091,0.0085,0.0052

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Very low resolution data set
by Xiang Li 03 Jul '13

03 Jul '13

Hi everyone, I am working on a very low resolution data set (14 A). It is a designed DNA crystal and unit cell size & symmetry fit well with the assumption. When I do the refinement I found the Rfree is extreme high, ~0.49 while Rwork is about 0.4. But the model seems fits in well with the density map. I have collected different datasets, and it gives about the same MR result for different sets. I do not have any experience to work with low resolution data. Here I have a few questions: 1 What is the expected Rfree and Rwork for such low resolution data? I looked up PDB bank, and there is a 11.5A crystal with Rfree=~0.4. But not sure whether there is a kind of value for Rfree to consider the refinement works or not. 2 There might be overfit problem during the refinement. Currently what I did is to optimize the weight with PHENIX gui, add restraints between basepairs and NCS restraint. I tried to manually adjust the weight, but seems the optimized weight gives the best result. Are there other things I should try? 3 How to confirm that the result is real? There will be larger than usual error for such low resolution data, and what the supposed range should be? Thanks a lot for your suggestions and help! Sincerely, Xiang

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omit map for protein-DNA complex
by Wei Shi 02 Jul '13

02 Jul '13

Hi guys, I've been trying to generate the omit map for a protein-DNA complex structure using Phenix. I don't know why it takes forever to run and didn't seem like to finish at all.... The resolution of the dataset is 3.2A. Omit map type: simulated annealing. Omit region: composite. And, for the corresponding apo-protein structure, the simulated annealing omit map was generated within 2 or 3 hours on the same computer cluster. Let me know whether you have any idea about what might go wrong and whether there is anything I could do.... Thank you so much! Best, Wei

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Bias in Rfree
by "Weiergräber, Oliver H." 02 Jul '13

02 Jul '13

Hello, while refining a structure with NCS, I was re-considering this paper from Michael Chapman's group: Fabiola F, Korostelev A, Chapman MS. Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry. Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):227-38. In essence, they suggest to exclude from the working set reflections that are (1) related to a test reflection by NCS (2) adjacent to a test reflection and its NCS mates in reciprocal space They have implemented this strategy in a CNS module (R-free2005), but the software is no longer actively supported. Does anybody know if something similar has ever been implemented in other software packages such as phenix? Or am I missing any significant downsides of the approach - apart from a reduction of the working set? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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