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Re: [phenixbb] HKL2000 behaved weirdly
by Mengbin Chen 20 Aug '13

20 Aug '13

Sorry for being late in replying, but thank you all for your suggestions! The resolution is ~3 angstroms, so it was quite easy to pick more than 100 peaks for indexing. So I tried to index ~5-6 images at the same time as you suggested, the Bravais Lattice window appeared (and I reset the beam center too), but the unit cell dimensions were ~10 angstroms along one axis, which was not appropriate since the protein is around 40 kDa. I tried to manually pick peaks for indexing, still cell dimensions were too small to be properly assigned. I feel the crystal has got severe problems of multiple lattices and high mosaicity at the same time, which made it hard to index. I am still playing around with the dataset to see if I can get any luck with it, so I'll let you know if I can work this out. Mengbin On Fri, Aug 16, 2013 at 12:18 PM, Noinaj, Nicholas (NIH/NIDDK) [F] < noinajn(a)niddk.nih.gov> wrote: > Mengbin, > > > This happens in HKL2000 with tough datasets. The data can sometime appear > to be very nice, possibly some high mosaicity, but still not process > properly. I have seen this many times. As mentioned already, the next > step is to start trying different things to get the data to process. > WIthout knowing more about resolution, etc, here is a few things to try. > > 1- Check and the double check the beam center. Then, check it again! > With troublesome datasets, this is EXTREMELY important. In HKL2000, > everytime you hit Abort Refinement, you have to reset the beamcenter again. > SO monitor the beam center and everytime it gets too far away from the > actual numbers, reset it. > > 2- you want to try to have roughly 100 peaks for indexing at minimum (if > possible), so change the resolution limits to 15 ang - 4 ang, then retry > indexing. IF this does not work, try 15-5ang, then 12-5, then 10-5, etc. > > 3- If #2 doesn't work, then you can alway try indexing using multiple > frames, esp if you don't have a enough peaks on the first frame. To do > this, please see the HKL2000 manual, or let me know, i can send you some > screenshots or give you a call to guide you via phone. here, you can use > 5-10 frames for indexing if needed. > > 4- as a last option, you can always manually select your peaks. i have had > this work nicely in the past, but again, last option. > > 5- you could try other data processing programs too such as MoSFLM, XDS, > Xia2, etc. > > If you still don't get it working, i am more than happy to take a quick > look. Just send me one of your frames to analyse. Of course, everything > will be strictly confidential. Thanks in advance and good luck! > > > > > Cheers, > Nick > > > > ________________________________ > From: Mengbin Chen [mengbinc(a)sas.upenn.edu] > Sent: Thursday, August 15, 2013 3:12 PM > To: PHENIX user mailing list > Subject: [phenixbb] HKL2000 behaved weirdly > > Dear All, > > I used HKL2000 to index my data, but weird things happened: after I hit > peak search, the data were selected to index, and I chose primitive > triclinic to continue. After I hit refine, the circles for peak search > disappeared, and if I hit "Bravais Lattice", the table would not show up, > which meant that I could not proceed to refine in the potentially correct > Bravais Lattice. I don't know if anyone else has encountered this problem > before, so any suggestions would be greatly appreciated! > > Thank you in advance, > Mengbin > > -- > Mengbin Chen > Department of Chemistry > University of Pennsylvania > -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Preferred treatment of residues with no electron density
by Mark Saper 20 Aug '13

20 Aug '13

What is the preferred method for handling missing residues or residues with zero occupancy, in terms of PBD submission? I see three options: Remove them from the model set occupancy=0 and flag in REMARKs 475 and 480 keep occupancy=1 and allow the temperature factors to climb I have a disordered region in my molecule which I am restraining to a portion of a structure in which that region is well resolved. There are several residues that have no density in the current refinement, yet I want to keep them in the model. Suggestions? Mark _______________________________________________ Mark A. Saper, Ph.D. Department of Biological Chemistry, University of Michigan Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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a question on LSTc refinement
by fn1＠rice.edu 20 Aug '13

20 Aug '13

Hi all, I read some previous post on LSTc [SIA(alpha2-6)GAL(beta1-4)NAG] refinement, but i still cannot figure out how to refine it in PHENIX. In the current version of phenix, i still could not find the ALPHA2-6 link. Does anybody have such experience? Another question is that, sialic acid (SIA) is in the monomer library of phenix. But when i run on the pdb directly, it will give the error information like, "unknown bond type for O1A and O1B". Though this error could be solved by provided the cif file generated by phenix.elbow. Thank you very much! Fengyun

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Ensemble refinement, starting water structure and alternative conformations
by Joseph Noel 19 Aug '13

19 Aug '13

Is it important (or at least useful) to remove any waters before initiating ensemble refinement wherein the waters are located in what is obvious electron density for alternative conformations of side chains? Would the presence of such waters possibly result in ensemble refinement NOT modeling the alternative conformations? ______________________________________________________________________________________ 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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Density modification using partial model phase
by Yi xing 17 Aug '13

17 Aug '13

Does mtz file from phenix.refine report FOM? If not, is there a way to have FOM listed in the mtz file. I am trying to use the mtz from the phenix refined model as the input of the ccp4 density modification (DM) or Dmmulti. For example, mtz file from Phaser molecular replacement has all the columns to run the DM. Many thanks for any help or comments! Best, yi

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HKL2000 behaved weirdly
by Mengbin Chen 16 Aug '13

16 Aug '13

Dear All, I used HKL2000 to index my data, but weird things happened: after I hit peak search, the data were selected to index, and I chose primitive triclinic to continue. After I hit refine, the circles for peak search disappeared, and if I hit "Bravais Lattice", the table would not show up, which meant that I could not proceed to refine in the potentially correct Bravais Lattice. I don't know if anyone else has encountered this problem before, so any suggestions would be greatly appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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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

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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

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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 * ************************************************

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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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