- phenixbb - phenix-online.org

AutoSol error
by Luca Pellegrini 10 Jan '13

10 Jan '13

AutoSol (phenix 1.8.1-1168) stops at the build stage with the following message: *** ERROR MESSAGE: The cell appears to have changed during the run Original cell: [49.22, 91.325, 103.285, 113.16, 97.64000000000001, 76.74] New cell : [49.173301696777344, 92.32479858398438, 103.37100219726562, 66.54070281982422, 82.29070281982422, 76.58550262451172] If running from a script, please specify the space group in the input file. The incorrect space group may be coming from another wizard... *** Can you please advice as to what might be wrong? I am running AutoSol from the GUI and it did pick up the space group from the mtz file. What AutoSol refers to as the 'new cell' is actually my original cell. I was running two AutoSol jobs simultaneously from two mtz files with the same cell dimensions, and they both failed with the same message. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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DEN refinement and reference model
by Luca Pellegrini 08 Jan '13

08 Jan '13

Phenix.den_refine (1.8.1-1168) stops and complains that: "Sorry: Reference model contains SEGIDs that do not match the working model." I have four chains in both working and reference model, ordered in the same way (A to D). Chains A and C are the same molecule, and chains B and D are also the same. Can you please advice? Some of the chains in the reference model contain more residues, is this a problem? Thanks for your help. Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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dev-1261 wizard.test fail
by Morten Groftehauge 08 Jan '13

08 Jan '13

Hi guys, I just updated Rosetta to 3.4 and it seems to have compiled correctly (at least no error interruptions). I've done this enough to not be satisfied by that and ran > phenix_regression.wizards.test_command_line_rosetta_quick which goes past the Rosetta tests correctly but fails at ================================================================= Running test_prerefine ------------------------------------------------------------ Numbers do not match: 0.47825 0.53601 r {{ 0.87799 0.06946 -0.47362} {-0.02049 0.99396 0.10779} { 0.47825 -0.08494 0.87411}} --- r {{ 0.84375 0.06393 -0.53291} {-0.02789 0.99676 0.07541} { 0.53601 -0.04877 0.84280}} ------------------------------------------------------------ FAILED See log files test_prerefine/test_prerefine.log test_prerefine/test_prerefine_current.log ================================================================= Running test_prerefine_double OK ================================================================= Running test_prerefine_no_data ------------------------------------------------------------ Numbers do not match: 0.47825 0.53601 r {{ 0.87799 0.06946 -0.47362} {-0.02049 0.99396 0.10779} { 0.47825 -0.08494 0.87411}} --- r {{ 0.84375 0.06393 -0.53291} {-0.02789 0.99676 0.07541} { 0.53601 -0.04877 0.84280}} ------------------------------------------------------------ FAILED See log files test_prerefine_no_data/test_prerefine_no_data.log test_prerefine_no_data/test_prerefine_no_data_current.log ================================================================= When I look in the log there are no error messages. I don't need to prerefine so I'm good but I still find it weird. I tried again with Rosetta 3.3 and got no error flags. Is it because the quick tests are checking the result against the results that you got earlier and the algorithm has been changed between 3.3 and 3.4? Cheers, Morten PS Really enjoyed the talks at the CCP4 study weekend. -- Morten K Grøftehauge, PhD Pohl Group Durham University

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mr_rosetta and disulphide bonds
by Morten Groftehauge 07 Jan '13

07 Jan '13

Hello again, I forgot my important question in all my "this seems to be working but the test says it doesn't"-drama: How do I specify disulphide bonds for MR_rosetta? I know it keeps them if they are in the input model but disulphides are generally poorly conserved, especially in the %identity range where mr_rosetta is the most useful. According to the changelog this feature should be available in the latest dev. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Ph.D. position at Lund University
by Derek Logan 07 Jan '13

07 Jan '13

A 4-year PhD position is available in the groups of Dr. Derek Logan and Prof. Ulf Ryde at the Dept. of Biochemistry and Structural Biology and the Dept. of Theoretical Chemistry at Lund University, Sweden. The project is sponsored by the European Spallation Source and will also involve the participation of ESS scientists. The PhD student will work on structural and theoretical studies of protein-ligand interactions, using the carbohydrate binding protein galectin-3 as a model system. Structural studies will be conducted principally using neutron crystallography in combination with X-ray crystallography at very high resolution (< 0.9 Å). The work will include production of crystals of suitable size for neutron diffraction, data collection at various neutron sources around the world, data processing and modelling. The theoretical studies will be conducted in Ulf Ryde's group at Theoretical Chemistry. We will develop methods to combine crystallographic refinement and quantum mechanical calculations. In addition, we perform molecular dynamic simulations and estimates of binding affinities using free-energy perturbation. The project is part of a larger network at Lund University including organic chemists, medical scientists and NMR experts, dedicated to a fundamental understanding of protein-ligand interactions in general and galectin inhibition in particular. The candidate must have bachelor's degree in an appropriate subject (preferably chemistry) and should ideally have previous experience in structural biology, both theoretical and practical. The candidate should also have good knowledge of theoretical chemistry. Experience of quantum chemistry, statistical mechanics and simulations is an advantage. The deadline for application is 31st January 2013. For more information on the eligibility requirements, please see: http://admin.lu.se/o.o.i.s?id=22598&Dnr=511988&Type=E Application should be made using the link in the right hand column of this web page. For informal enquiries on the project contact: Derek Logan, Associate professor +46 46-2221443 derek.logan(a)biochemistry.lu.se Ulf Ryde, Professor +46-2224502 ulf.ryde(a)teokem.lu.se http://www.cmps.lu.se/ http://www.teokem.lu.se/ http://www.chem.lu.se/People/galectins_in_Lund/ http://www.esss.se

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Deadline: 4 February -- Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 04 Jan '13

04 Jan '13

We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Fwd: WCPCW 21
by Nathaniel Echols 03 Jan '13

03 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Thu, 3 Jan 2013 10:42:14 -0800 Subject: WCPCW 21 Dear All, Happy New Year! The West Coast Protein Crystallography Workshop is fast approaching (March 17th). The site (wcpcw.org) is up, registration is open and the option to pay by credit card is now available. The conference has a long tradition of methods development and organized as such to facilitate discussion and colloboration. We are especially interested in having speakers that are doing the ‘real’ work - graduate students, postdocs and staff scientists! We are also honored having Prof. Wayne Hendrickson as our keynote speaker. Prof. Hendrickson has made seminal contributions to the field including efforts in phase combination (Hendrickson-Lattman coefficients), incorporation of stereochemical constraints in protein refinement (e.g., PROLSQ – the predecessor to many of the refinement programs we now use), and the development of MAD phasing (including the development of selenomethionine incorporation). In addition, Prof. Hendrickson’s lab has produced a large number of biologically important structures including the HIV caspid GP120 bound to CD4, the first tyrosine kinase structure (Lck), and many, many others. We look forward to seeing you in Monterey! Best, John

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Anomalous group refinement question
by Pawel Grochulski 03 Jan '13

03 Jan '13

Dear all, Instruction says: Anomalous groups refines the anomalous coefficients f' and f'' for anomalously scattering atoms such as Se or heavy metals; it is only appropriate if you have anomalous data (I+/I- or F+/F-). How do I indicate which atoms to be considered? Thank you for your help. Happy New Year. Pawel ____________________ Dr. Pawel Grochulski, D.Sc. Canadian Macromolecular Crystallography Facility (cmcf.lightsource.ca<http://cmcf.lightsource.ca/>), Canadian Light Source Inc., 44 Innovation Boulevard, Saskatoon, SK S7N 2V3, Canada. Phone: +1 (306) 657-3538, Fax: +1 (306) 657-3535. Adjunct Professor of Pharmacy, College of Pharmacy and Nutrition, University of Saskatchewan (www.grochulski.com<http://www.grochulski.com/>) __________________________________________________________________________________________

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

27 Dec '12

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

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

22 Dec '12

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

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

22 Dec '12

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

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Problems with rosetta_mr
by Yoni Haitin 21 Dec '12

21 Dec '12

Hello all, I have been trying (desperetly) to run the Rosetta_MR. I have encountered some problems with my data, so I switched to the "HNP3-mr-rosetta" tutorial dataset. I followd the debugging suggestions in the instructions webpage with no improvement. It seems that I have a problem in the rebuild stage. Attached are the RUN_FILE_1.log from REBUILD_IN_SETS_5 and ../WORK_1/rebuild.log. The edited_align.ali file cannot be opened for some reason. Another issue is that the map used is being taken from "overall_best_denmod_map_coeffs_nf.map" instead of "cycle_best" (as is in the tutorial's mr_rosetta_output log). this seems to produce an error (last log file attached). What should I do next? Thank you, Yoni Parameters taken from: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/PARAMS_1.eff # mr_rosetta_rebuild # # Run automr mr_rosetta_rebuild with rosetta # Type phenix.doc for help Values of all params: mr_rosetta_rebuild { input_files { model = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb" map = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map" seq_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/EDITED_1dfn.seq" hhr_files = None alignment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali" model_info_file = "" fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_09_05.200_v1_3.gz" fragment_files = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/phaser_rosetta/aat000_03_05.200_v1_3.gz" fragment_files_chain_list = None fragment_files_9_mer_by_chain = None fragment_files_3_mer_by_chain = None use_dummy_fragment_files = False sort_fragment_files = True } output_files { log = "mr_rosetta_rebuild.log" params_out = "mr_rosetta_rebuild_params.eff" } directories { temp_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" workdir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1" gui_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta" top_output_dir = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14" rosetta_path = "/Users/administrator/rosetta_3.4" rosetta_binary_dir = "rosetta_source/bin" rosetta_binary_name = "mr_protocols.default.macosgccrelease" rosetta_script_dir = "rosetta_source/src/apps/public/electron_density" rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/" rosetta_database_dir = "rosetta_database" } rosetta_rebuild { run_rosetta_rebuild = True stage_to_rebuild = "rescored_mr_solution" max_solutions_to_rebuild = 5 min_solutions_to_rebuild = 1 llg_percent_of_max_to_keep = 50 rosetta_models = 20 chunk_size = 1 edit_model = True superpose_model = False } rosetta_modeling { map_resolution = 3 map_grid_spacing = 1.5 map_weight = 1 map_window = 5 include_solvation_energy = True weights_file = "" } crystal_info { resolution = 0 space_group = "P 21 21 2" chain_type = *PROTEIN DNA RNA ncs_copies = 1 } control { verbose = False debug = False raise_sorry = False dry_run = False nproc = 1 group_run_command = "sh " queue_commands = None condor_universe = "vanilla" add_double_quotes_in_condor = True condor = None one_subprocess_level = None single_run_command = "sh " last_process_is_local = True background = True ignore_errors_in_subprocess = True check_run_command = False max_wait_time = 100 wait_between_submit_time = 1 wizard_directory_number = 14 n_dir_max = 100000 number_to_print = 5 write_run_directory_to_file = "/Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/INFO_FILE_1" resolve_command_list = None start_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \ similarity refine_top_models average_density_top_models \ relax_top_models autobuild_top_models \ setup_repeat_mr_rosetta repeat_mr_rosetta stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \ similarity refine_top_models average_density_top_models \ relax_top_models autobuild_top_models \ setup_repeat_mr_rosetta repeat_mr_rosetta clean_up = False } non_user_params { file_base = "1zmm_mr.1" print_citations = False highest_id = 10 is_sub_process = True dummy_autobuild = False dummy_refinement = False dummy_rosetta = False prerefine_only = False skip_clash_guard = True correct_special_position_tolerance = None comparison_mtz = "" labin_comparison_mtz = None write_local_files = False rosetta_fixed_seed = None } } Starting mr_rosetta_rebuild Date: Thu Dec 20 14:44:49 2012 Directory: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5 HOST = ZagottasMacPro.local HOSTTYPE = intel-mac MACHTYPE = x86_64 OSTYPE = darwin VENDOR = apple USER = administrator PID = 36828 Checking rosetta paths: rosetta binary: /Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease database_dir: /Users/administrator/rosetta_3.4/rosetta_database script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/public/electron_density pilot_script_dir: /Users/administrator/rosetta_3.4/rosetta_source/src/apps/pilot/frank/ Changing to work directory: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1 Rebuilding the model /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb with rosetta Rebuilding model using map at resolution of 3.0 A Generating 20 rebuilt models ================================================================================ Reading model from /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/1zmm_mr.1.pdb ================================================================================ ALIGNMENT LINES: ## TARGET 1zmm_ # hhsearch scores_from_program: 0 1.00 0 DCYCRIPACIAGERRYGTCIYQGRLWAFCC 1 -CYCRIPACIAGERRYGTCIYQGRLWAFCC -- Trying to adjust the PDB sequence from alignment file: -CYCRIPACIAGERRYGTCIYQGRLWAFCC to match the actual PDB sequence: YCRIPACIAGERRYGTCIYQGRLWAFCC New alignment line 4 for PDB: 1 --YCRIPACIAGERRYGTCIYQGRLWAFCC Start position of target sequence in sequence file: 0 Aligned model for comparison: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /Users/administrator/Yoni/Rosettal tutorial data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_5/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** --- Here is ../WORK_1/rebuild.log: core.init: Mini-Rosetta version unknown from unknown core.init: command: /Users/administrator/rosetta_3.4/rosetta_source/bin/mr_protocols.default.macosgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=345021854 seed_offset=0 real_seed=345021854 core.init.random: RandomGenerator:init: Normal mode, seed=345021854 RG_type=mt19937 ERROR: Warning: can't open file /Users/administrator/Yoni/Rosettal/ tutorial/ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_1/edited_align.ali! ERROR:: Exit from: src/core/sequence/util.cc line: 380 --- core.init: Mini-Rosetta version exported from unknown core.init: command: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_source/bin/mr_protocols.default.macosgccrelease @rebuild.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-340184367 seed_offset=0 real_seed=-340184367 core.init.random: RandomGenerator:init: Normal mode, seed=-340184367 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pdb_pair_stats_fine core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_n core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/P_AA_pp core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/Rama_smooth_dyn.dat_ss_6.4 core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/env_log.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cbeta_den.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/pair_log.txt core.io.database: Database file opened: /Users/administrator/rosetta_3.2/rosetta3.2_bundles/rosetta_database/cenpack_log.txt core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.electron_density.ElectronDensity: Loading Density Map core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map /Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map. Not loading map. core.scoring.electron_density.ElectronDensity: [ ERROR ] Error loading density map named '/Users/administrator/Yoni/Rosettal\ tutorial\ data/HNP3-mr-rosetta/MR_ROSETTA_14/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_5/WORK_1/junk/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoBuild_run_1_/overall_best_denmod_map_coeffs_nf.map' -- Yoni Haitin, Ph.D. Department of Physiology and Biophysics University of Washington Seattle, WA 98195-7290 Email: yonihaitin(a)gmail.com Email(2): haitinyo(a)uw.edu

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problem about phase caculate
by yzhao 19 Dec '12

19 Dec '12

Hi everyone, I have came into a problem recently. My structure was solved by MAD and a crude model was built manually. Several peak data sets were collected, resolution is about 4A-4.2A. The heavy atom can be located by anomalous difference fourier. I feed the initial phase or heavy atom sites, and the peak data set to phenix. However the map after DM is too bad. The density is very strange. I don't know what's the problem? In addition, how to define protein mask at phenix autosol for density modification? Thanks in advance. -- Yan Zhao, M.Phil. National Laboratory of Protein Sciences Institute of Biophysics Chinese Academy of Sciences 15 Datun Rd. Beijing, 100101 China

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composite simulated annealing omit map.
by Appu kumar 18 Dec '12

18 Dec '12

Dear members, please guide me which mtz. file i should use to make composite SA omit map. Out of two mtz file which one should i consider, Initial mtz file which is an output of scalepacktomtz programme or the recent mtz file which is an output of phenix/refmac after refinement. What is the sigma level at which these map should be made.? Thanks in advance Appu

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fwd: WPCPW 21
by Nathaniel Echols 14 Dec '12

14 Dec '12

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Cc: Date: Fri, 14 Dec 2012 13:03:49 -0800 Subject: WCPCW 21 All, Just wanted to inform you that registration for the West Coast Protein Crystallography Conference is now open. Wayne Hendrickson will be the keynote speaker! The meeting, March 17th to the 21st at the Monterey Plaza and Spa, emphasizes all aspects of protein/macromolecular methods and developments. The fees are all inclusive - registration, room, food and social hours. Please see www.wcpcw.org. Happy Holidays. Best, John

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PDB header
by Eric Girard 13 Dec '12

13 Dec '12

Dear phenix users, I currently try to deposit a structure within PDBe. I discovered that the pdb header has missing information, in particular K_sol, B_sol, Wilson B, Estimate_errors, overall anisotropic B value . Is it linked to the TWIN_LSQ_F target used (Phenix version 1.8.1_1168) or to something wrong I did? How can I recover these information? Thanks for your help. Best regards. Eric. -- *************************************************************** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA-CNRS-UJF-PSB 41, Rue Jules Horowitz 38027 Grenoble Cedex 1, France Phone: +33 (0)4 38 78 96 45 Fax: +33 (0)4 38 78 54 94 Web site: http://www.ibs.fr/ ***************************************************************

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Refinement and glycosylation.
by Jan van Agthoven 12 Dec '12

12 Dec '12

Hi everyone, I refined my structure using phenix.refine and used the following parameters to define the ASN-NAG link: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resseq x residue_selection_2 = chain A and resname ASN and resseq y } However I would like the glycosylation to be Beta (NAG in Beta configuration). How can I define this in the parameter file? Thanks,

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pathological case with soaking
by Appu kumar 12 Dec '12

12 Dec '12

Respected members,, I have one question regarding soaking. Binding of the substrate to enzyme leads to active site closure. So if we are soaking the enzyme crystal with the substrate, and collecting the data and solving the structure, then how would one distinguish the existence of apo and substrate bound form of enzyme in same crystal. I meant to say, soaking may cause the crystal to have quasi-apo-enzyme and quasi-substrate-enzyme complex existing together. Is there any way to take care of such pathological condition during data processing, or structure solving? . I would highly appreciate your help and looking forward to get valuable advices. Please graduate me in this kind of weired situation. Thank you Appu

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Re: [phenixbb] phenix and weak data
by Douglas Theobald 12 Dec '12

12 Dec '12

Hi Ed, Thanks for all the info, its very useful. So I have two questions now. What is the evidence, if any, that the exptl sigmas are actually negligible compared to fit beta (is it alluded to in Lunin 2002)? Is there somewhere in phenix output I can verify this myself? And, in comparison, how does refmac handle the exptl sigmas? Maybe this last question is more appropriate for ccp4bb, but contrasting with phenix would be helpful for me. I know there's a box, checked by default, "Use exptl sigmas to weight Xray terms". Cheers, D On Dec 10, 2012, at 1:04 PM, Ed Pozharski <epozh001(a)UMARYLAND.EDU> wrote: > On 12/06/2012 05:35 PM, Douglas Theobald wrote: > >> However, I was surprised to hear rumors that with phenix "the data are not properly weighted in refinement by incorporating observed sigmas" and such. > Douglas, > > Up to a certain point in its derivation, maximum likelihood target is > exactly the same in all implementations. Where Lunin/cctbx/phenix > approach is different is that it derives analytical expressions for > model error parameters by optimization of the maximum likelihood target > itself with respect to these. It's a clever approach, except that it > does not work unless one ignores experimental errors. > > A minimization target contains essentially a difference between > calculated and observed structural amplitudes (properly scaled etc). > For each reflection it must be properly weighted by combined > uncertainty, which includes both model error and experimental error. > Assume that former is much larger than the latter which can then be > ignored. Both errors are now combined in a single parameter (per > resolution shell, called beta), which can be calculated analytically. > Once this is done, we go back and check - and indeed, this combined > model error is larger than the experimental one. > > There are few interesting consequences of this. > > First, it seems clear that weighting every reflection in a resolution > shell the same way is a compromise. One expects less precisely measured > reflections should be weighted down. But the effect may be small. > > Second, mathematically it turns out that the target value (towards which > Fc is pushed) for some reflections should be set to exactly zero. The > cutoff is Fo<sqrt(es*beta). Quote from Lunin et al., 2002: > > "...in this case, the likelihood-based target fits the calculated > magnitude to the zero value (Fs*=0) regardless of the particular value > of Fobs." > > Third, one is tempted to interpret the beta parameter as the model > variance. The problem is sqrt(beta) ends up significantly higher than > one would expect from the R-values. This, imho, poses a bit of a problem > in light of the second issue - resetting Fs* to zero for "weak > reflections". If beta ends up overestimated for whatever reason, then > those reflections aren't that weak anymore. > > Yet, the refinement still seems to work just fine. So perhaps > overestimated model error is not a big deal in that respect. Indeed it > is not. In fact, one can multiply beta by arbitrary number, and the > relative weight applied to individual reflections in maximum likelihood > will remain roughly the same. So while it provides robust > resolution-dependent weighting, the absolute value of beta parameter is > not easily interpreted (as absolute model error). > > Hopefully all is well in sunny Waltham, > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > >

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Postdoctoral position in crystallography of the CFTR ion channel
by Machius, Mischa Christian 12 Dec '12

12 Dec '12

On behalf of a collaborator, I'd like to bring this open position to your attention. Postdoctoral position available in the laboratory of Jack Riordan, Dept of Biochemistry and Biophysics and Cystic Fibrosis Center, University of North Carolina at Chapel Hill. To join and provide a major contribution to a team working on the production, purification and characterization of the CFTR ion channel protein for crystallization and X-ray crystallography. Required experience working with membrane proteins and lipids and/or protein crystallization. Focus will be on crystallization in meso in collaboration with experts in that technology. Contact: jack_riordan(a)med.unc.edu<mailto:[email protected]> The University of North Carolina is an equal opportunity employer. ----------------------------------------------------------------------- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: machius(a)med.unc.edu<mailto:[email protected]>

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SA Fo-Fc omit map
by Mengbin Chen 12 Dec '12

12 Dec '12

Dear Phenix Users, I have been playing around with Phenix AutoBuild GUI to generate a fo-fc sa omit map of the ligand in a protein structure, and I have the input files as follows: output.mtz (data type:experimental data) ligand.pdb (data type: omit box atoms & ligands) ligand.cif (data type: restraints of the ligand) protein.pdb (data type: starting model) omit map type: simulated annealing omit region: omit around PDB fie I have set the occupancies of all ligand atoms zero and deleted the ligand coordinates in my starting model. After the run finished and I checked the refined coordinates and map.mtz in COOT, I found that there was no electron density around the ligand while the protein model was in electron density, which was exactly opposite of what I wanted before. Furthermore, I have 3 Mg2+ ions in protein.pdb file, all of which moved away from where they were after the refinement run, which was not wanted either. Could anyone tell me how to do the sa omit map of ligand correctly? Thanks in advance! Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Re: [phenixbb] Fwd: parameters for averaged kick maps
by Pavel Afonine 10 Dec '12

10 Dec '12

Hi Jose, kick-map related parameters in ordered_solvent scope of parameters are leftover that I forgot to remove back when I was working on it. So you can see it as a minor bug. And yes, you can't change them. Sorry about delayed answer (I saw the email on phenixbb but did note reply immediately and it sank in the flood of other stuff). Pavel On 12/10/12 11:04 AM, Jose M de Pereda wrote: > Dear Phenix Team, > > Last week I sent an e-mail to the phenixbb regarding the parameters > that control de generation of averaged kick maps. Unfortunately, I > have not received any feedback from the community. > > I wonder if you could give me some help on this subject. > > Probably, the calculation of averaged kick maps is already very well > optimized in phenix.refine and phenix.maps. Yet, I am still curious. > > Thanks a lot in advance > All the best > > Jose > > > -------- Original Message -------- > Subject: [phenixbb] parameters for averaged kick maps > Date: Tue, 04 Dec 2012 10:12:46 +0100 > From: Jose M de Pereda <pereda(a)usal.es> > Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > Dear all, > > I would like to compare averaged kick maps obtained using different “kick sizes”. > Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? > > In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: > kick_map { > kick_size = 0.5 > number_of_kicks = 100 > } > But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. > > Related with this issue, does phenix.refine always use the same kick > size or does it adjust it ad hoc (e.g. based on ML error estimates)? > > Thanks a lot, > Jose > > > -- > ------------------------------------------------------------ > Jose M de Pereda, PhD > Instituto de Biologia Molecular y Celular del Cancer (IBMCC) > Spanish National Research Council - University of Salamanca > Campus Unamuno s/n > E-37007 Salamanca, Spain > Phone: +34-923-294817 > Fax: +34-923-294795 > http://xtal.cicancer.org/ > ------------------------------------------------------------ > >

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Simulated annealing map
by Appu kumar 10 Dec '12

10 Dec '12

Thank you Terwilliger, Thomas for you quick reply, for guiding me on how to make simulated annealing omit map. Now i am able to make it but i have one question. i want to show the SA omit map of ligand with the map of omitted region around ligand. I tried it, i got the map also, but the omitted map of region around ligand is show in recatangular box which is not as great as of ligand inside the omitted region. Thank you

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Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 10 Dec '12

10 Dec '12

We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Real Space CC Raw Data
by Eddie Pryor 08 Dec '12

08 Dec '12

Hi, All, To satisfy a reviewer, I would like to include a supplemental figure that contains, among other things, Real Space CC for each residue. I was wondering where this raw data might be stored so that I can parse and create a graph with it. The only thing I could find was in the Refine_###_info.txt log file, but that only included values less than 0.7. I know that all of the residues / CC values can be listed through the GUI, but with ~900 residues in my ASU, this is something I do not want to do manually! Thanks! --Eddie Pryor

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How to make simmulated annealing omit map
by Appu kumar 07 Dec '12

07 Dec '12

Dear Users, I am refining a enzyme structure with ligand. I want to make the simulated annealing omit map of ligand including with 4 Angestron radius around the ligand. I am seeking your valuable advice to help me out. I know how to make omit map but i have not come accross making simmulated annealing omit map. I would appreciate your help. Thank you Appu

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Is this a Phaser bug or am I misinterpreting ?
by Phil Jeffrey 05 Dec '12

05 Dec '12

Phaser from CCP4 6.3.0 built via fink running on OSX 10.6.8 in 64-bit mode. This is a snippet from a much larger run, ongoing. In multiple instances the order of the LLG and the Z-score in the translation function are not in sync: (42.16, 40.23, 40.18 vs 5.14, 5.24, 4.82) and looks like the Z-scores are still shown in the peak rank order before rescoring, while the LLGs are after rescoring. SET #5 of 6 TRIAL #60 of 115 ---------------------------- Search Euler = 263.0 82.1 85.7, Ensemble = ensemb3 ANNOTATION: RFZ=3.6 TFZ=3.8 PAK=0 LLG=26 LLG=30 Known MR solutions SOLU SPAC C 1 2 1 SOLU 6DIM ENSE ensemb3 EULER 30.6 65.7 246.9 FRAC 0.90 0.00 0.17 BFAC -5.14 Grid sampling: 0.825029 Angstroms Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean) Top 360 translations before clustering will be rescored Calculating Likelihood for TF SET #5 of 6 TRIAL #60 of 115 0% 100% |=========================================================================| DONE Scoring 1 randomly sampled translations Generating Statistics for TF SET #5 of 6 TRIAL #60 of 115 0% 100% |==| DONE Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score Select all peaks There were 159 peaks # (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top 1 6 0.842 0.923 0.779 +42.16 5.14 0 2 52.58/ 52.58 2 3 0.369 0.865 0.553 +40.23 5.24 37 2 53.18/ 53.18 3 10 0.743 0.937 0.261 +40.18 4.82 48 2 50.69/ 50.69 #SITES = 159: OUTPUT TRUNCATED TO 3 SITES

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Re: [phenixbb] log files for refinement (was: completeness using Intensities vs. structure factor)
by Pavel Afonine 05 Dec '12

05 Dec '12

Hi Yarrow, thanks for sending log files. Completeness reported in log files reflects the content of input MTZ data files: *32.log:* (...) F-obs: (...) Miller array info: (...)/reflectionsFreeR_1.38A.mtz:F_New(+),SIGF_New(+),F_New(-),SIGF_New(-),systematic_absences_eliminated Observation type: xray.amplitude Type of data: double, size=325598 Type of sigmas: double, size=325598 Number of Miller indices: 325598 Anomalous flag: True Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 (...) and *35.log:* (...) I-obs: (...) Miller array info: (...)/reflectionsFandIFreeR_1.38A.mtz:IMEAN_New,SIGIMEAN_New,systematic_absences_eliminated Observation type: xray.intensity Type of data: double, size=181940 Type of sigmas: double, size=181940 Number of Miller indices: 181940 Anomalous flag: False Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 (...) The numbers above are reported before anything else is done, that is they reflect exactly what's in input MTZ files. Somehow you managed to loose ~10% of data when converting Iobs into Fobs. How did you do this conversion? In theory this is possible since French&Wilson Iobs->Fobs conversion may result on some number of reflections lost. Note, when phenix.refine does IMEAN->Fobs conversion (35.log file) this does not result in ~10% loss. So based on looking at log files I can say it's not phenix.refine that manipulated your data or reported it wrong. You lost reflections at previous steps. Pavel On 12/4/12 4:57 PM, Yarrow Madrona wrote: > Hi, > > Here are the log files for refinement you asked for. > > 35.log is refined with Intensities. The MTZ file has a slightly different > name but it is the same MTZ. One had Intensities taken out of it because I > didn't think I needed them any longer. > > 32.log is refined with structure factors. Intensities were removed. > > Thanks for your help! > > -Yarrow > > >

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completeness using Intensities vs. structure factor
by Yarrow Madrona 05 Dec '12

05 Dec '12

Hi, (Phenix v.1.8.1-1168) I recently refined a structure using experimental Intensities and compared it to the same structure refined with calculated structure factors. I know if you provide intensities Phenix.refine will convert to structure factors. I am not sure if it runs truncate or what. Anyway, I get this in the log file which matches my completeness in the scala log file: Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 When I run using structure factors (Truncate run in Scala) I get the following: Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 Perhaps Scala did not merge anomolous and non-anomolous data? This does not may a whole lot of sense to me. Is some data thrown out? Can someone explain? Thank you. -- 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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parameters for averaged kick maps
by Jose M de Pereda 04 Dec '12

04 Dec '12

Dear all, I would like to compare averaged kick maps obtained using different “kick sizes”. Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: kick_map { kick_size = 0.5 number_of_kicks = 100 } But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. Related with this issue, does phenix.refine always use the same kick size or does it adjust it ad hoc (e.g. based on ML error estimates)? Thanks a lot, Jose -- ------------------------------------------------------------ Jose M de Pereda, PhD Instituto de Biologia Molecular y Celular del Cancer (IBMCC) Spanish National Research Council - University of Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294817 Fax: +34-923-294795 http://xtal.cicancer.org/ ------------------------------------------------------------

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table 1
by So Jay 04 Dec '12

04 Dec '12

Hi, I was using generate table 1 utility in phenix-1.8.1-1168. The data was processed with HKL2000 and model was refined using Autobuster. In the table I find two entries for Multiplicity and R-sym were blank.I was wondering if there is any particular reason for this. ThanksJay

2 2

Similar 2Fo-Fc maps, very different e/A^3 levels (absolute levels)
by Sam Stampfer 04 Dec '12

04 Dec '12

Dear Phenix group, I am trying to decide which electron density map to use for rebuilding my structure in Coot. Both 2Fo-Fc maps appear quite similar at the 1 sigma level but the absolute electrons per cubic Angstrom (e/A^3) is very different. When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot calls them absolute levels): Map #1 2Fo-Fc: 0.0044 e/A^3 Map #2 2Fo-Fc: 0.0832 e/A^3 Map #1 was generated using a twinning operator that is typically required for this crystal form. Map #2 was generated without the twinning operator and it tends to have slightly better 2Fo-Fc density, and there is a bit more density (or noise?) in the Fo-Fc map. The structure was refined in Phenix and gave a similar Rfree regardless of whether a twinning operator was used. What does it mean to have this 20-fold difference in electrons per cubic Angstroms for my maps? Which map should I use? Thanks for your help! -Sam PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3 level.

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pseudotranslation and twinning problem
by Rajeshwer Sankhala 03 Dec '12

03 Dec '12

I am new to crystallography. I have collected data for 26 kDa protein with a maximum resolution of 2.25A in I 41 space group. I have a poor model for molecular replacement (~15-20% identical). When i did xtriage run, it suggested -h,k,-l twinning law and indicated about pseudo-translation. Now when i am running Phaser for molecular replacement i am getting very low LLG (less than 100) and TFZ score (5-6). Can anyone suggest which parameters or setting i should use to improve my LLG score and get a best model for refinement. Thanks Raj

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dev-1227: problem reading in tls parameters from refmac or tlsmd
by Boaz Shaanan 02 Dec '12

02 Dec '12

Hi, In the TLS pulldown I tried to upload tls parameters from either refmac (.tls) or tlsmd (.tlsin) through the 'load' button, according to the suggestion in this section, but it complains about wrong format of the file. Am I doing something wrong? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Specify particular columns from data files on the command line
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all (again)- I'm trying to run DEN refinement in Phenix from the command line. How do I specify certain columns from multiple data files (in my case, 2 MTZ files) to be used? For example, the Rfree flags from one and the hkl data from the other. Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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DEN refinement
by Morten Groftehauge 30 Nov '12

30 Nov '12

Hi guys, Two quick questions about DEN refinement: 1) If gamma refines to 0 does that mean that I should run DEN refinement again with the output model? Or should I do a refinement and then another DEN? Since gamma = 0 the refinement should be allowed a possibility of moving the structure further towards the reference restraints in my mind. 2) If gamma refines to 1 it means that my reference model is inappropriate, right? Not really much of a question, I know. And I know that DEN refinement is in beta but it would be nice if you outputted the optimal gamma and weight for the refinement to the GUI. Actually it would be nice if the did that for geometry weights and xray weights too when one optimizes them. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Error starting Phenix on Linux
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all- After installing the latest version and release of Phenix (1.8.1-1168) onto our Linux workstation and setting the environment for bash, I get the following error upon trying to launch Phenix from the command line: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I've never seen this before (previous versions of Phenix have run fine on this machine) and don't know what this file is exactly and where it should be located. Anyone come across this and know if there is a fix (or if I'm just doing something stupid!). Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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Call for submissions for the Computational Crystallography Newsletter (CCN) January 2013
by Nigel Moriarty 30 Nov '12

30 Nov '12

Folks Calling for articles and short communications of interest to structural biologists. The deadline for publication in the January 2013 issue is 31 December, 2012 but if you can send me drafts before the 15th of December we can get started on generating proofs. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty, PhD 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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choosing Rfree set with NCS and twinning
by vincent Chaptal 30 Nov '12

30 Nov '12

Dear phenixbb, I am using the "reflection file editor" in phenix 1.8.1-1168 to generate my test set (with the GUI). I have NCS so I ticked the box "assign test set in thin resolution shells". I also have twinning, and want to have my Rfree not biased by twin related reflections. I guess the option "use lattice symmetry to generate test set" is the one I should use for this purpose? I couldn't find much information online about this option. No log file has been generated so I can't check what happened. I am supposing xtriage is ran in the background and if a twin law is found, then used to generate the test set. My output from xtriage is: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -k,-h,-l |PM| 0.249| 0.272| 0.246| 0.200| ----------------------------------------------------------------- And indeed if I check in mtzdmp the output mtz, reflections in the test set are related by (-k, -h, -l); disclaimer: I only checked in the plane (h,k,0). I would like to be sure my Rfree is generated correctly. Alternatively, what would happen when multiple twin laws are available? Is the most probale used? Is it possible to specify the editor which law to use? Thank you for your help. Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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DNA double helix with many molprobity bad clashes
by Benda, Christian 30 Nov '12

30 Nov '12

Hi, I am refining a protein-DNA complex at around 3 A with a standard b-form dsDNA. R-factors are around 24/20 (kinda low for the resolution). Originally, I placed the DNA using coot and now, after several rounds of refinement in phenix, I get a long list of bad clashes from molprobity validation (in phenix) that covers the whole length of the DNA and almost exclusively lists hydrogens from the ribose moiety (whether or not in contact with protein). My question is, - why is phenix.refine not taking care of these clashes (i.e. optimizes the structure such that they go away)?. Am I giving experimental contribution to high a weight (I have "optimize x-ray/stereochemistry" checked)? - if so, can I (and how) restrain geometry for the DNA a little more but leave the protein alone (and does that make sense)? thanks for any help Christian

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phenix.erraser error
by Russell Chan 29 Nov '12

29 Nov '12

Hi, I'm currently trying to use the new command, phenix.erraser, to refine my RNA structure. I generated a ccp4 map and removed the R-free flags, however it generates an error after its starts its first round of minimization. The command I use is: phenix.erraser <mypdb>.pdb <mymap>.ccp4 The error generated is: ################################### Starting SWA_rebuild_erraser.py... Output pdb will be...precursor_chi_erraser.pdb Create temporary directory /home/Russ/Desktop/erraser_test/precursor_chi_erraser_temp/... fixed_res_final in Rosetta pdb file = [] cutpoint_final in Rosetta pdb file = [1, 2, 3, 4, 12, 15, 19, 20, 21, 25, 30, 37, 38, 49, 54, 58, 68, 69, 72, 79, 83, 84, 105, 108, 109, 122, 124, 125, 130, 133, 134, 137, 140, 143, 146, 158, 160, 161, 168, 170, 176, 179, 187, 189, 201, 204, 205, 216, 217, 228, 237, 239, 241, 245, 246, 268, 269, 273, 279, 283, 292, 293, 302, 305, 309, 311] extra_res_final in Rosetta pdb file = [] Starting whole-structure minimization 1... ******************* ERROR ENDING *************** Command 'phenix.python /home/sbgrid/programs/x86_64-linux/phenix/1.8.1-1168/phenix-1.8.1-1168/phenix/phenix/erraser/full_struct_slice_and_minimize.py -binary_name linuxgccrelease -map /home/<Russ>/Desktop/erraser_test/erraser_map.ccp4 -map_reso 2.0 -new_torsional_potential True -pdb minimize_0.pdb -out_pdb minimize_1.pdb > minimize_1.out 2> minimize_1.err' returned non-zero exit status 1 ******************* ERROR ENDING *************** Any help would be greatly appreciated! Thanks, Russell

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Nathaniel Echols 28 Nov '12

28 Nov '12

---------- Forwarded message ---------- From: Paul Emsley <pemsley(a)mrc-lmb.cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: Date: Wed, 28 Nov 2012 17:08:50 +0000 Subject: Re: [phenixbb] [COOT] CCP4 - Coot in Applications On 28/11/12 15:03, Antony Oliver wrote: > > Ok - annoying thing…. > > 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. > 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". It is not clear to me if you are, or are not using Bill Scott's binary... (it's the one I recommend for Macintosh). Paul.

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Antony Oliver 28 Nov '12

28 Nov '12

Ok - annoying thing…. 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSGetSurfaceBounds >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Ideas and suggestions welcome. I guess I could make sure that X11 is not running each time I invoke a script or run coot from the command line - but it's not exactly ideal. --> NB: Running Mac OS X, 10.7.5 - Lion. Please excuse the cross bulletin board posting, but I really do use quite a range of software across all program suites - and this method of delivering coot causes problems for many of the plugins/scripts (phenix and buster for example). With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Nov 27, 2012, at 11:32 AM, Antony Oliver wrote: > Thanks Charles - that seems to work..! > > Tony. > > --- > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > > email: antony.oliver(a)sussex.ac.uk > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > On Nov 26, 2012, at 10:19 AM, Charles Ballard wrote: > >> You could give >> >> /Applications/coot.app/Contents/Resources/script >> >> a go. >> >> Charles >> >> On 23 Nov 2012, at 12:20, Antony Oliver wrote: >>

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coordinate refinement and maps
by Subhani Bandara 27 Nov '12

27 Nov '12

Hi all, I am refining a protein with metal-ligand complexes. Is it possible to refine only y coordinates for an atom (on two fold) while keeping X and Z fixed using Phenix? Also is there a way to calculate something like anomalous difference-difference map (Anomalous Fobs - Anomalous Fcalc) to identify any additional atoms bound at metal sites. Thanks in advance for the help! Subhani

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cif file for modified peptide
by Feldkamp, Michael Dennis 27 Nov '12

27 Nov '12

I would like to generate a cif file for a peptide that is FITC labeled at the N-terminus and also contains an unnatural amino acid (dichloro phenylalanine). I've used phenix.elbow in the past to generate cif files for small molecule ligands but when I've run it I only get a cif file for the FITC. Any insight would be greatly appreciated, Michael Feldkamp

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MR_Rosetta prerefine
by Heather Condurso 26 Nov '12

26 Nov '12

Dear all, I am using mr_rosetta to run prerefinement of various starting models that all have pretty low sequence homology to my protein of interest (~15%). I ran it using the simple script from the manual: phenix.mr_rosetta \ seq_file=seq.dat \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 Its working fairly well, but obviously taking a long time to make 1000 models. Is there a log or score file somewhere that lists all of the rosetta scores as it is running? Right now all the pdb files in each different run have the format S_"original model name"__0001.pdb no matter what run it resulted from. Is there a way to make it unique for example with the actual run number in place of 0001? This makes it difficult to compare files in pymol. Thanks, Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

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Difficult MR with TNCS
by Ian Slaymaker 26 Nov '12

26 Nov '12

Dear Phenix Community, I am having difficulties solving a protein-DNA complex structure and was hoping for some ideas or strategies. My data diffracts to 3A and depending on how I index my data fits well into I4 or P4. I have also been exploring everything in lower space groups. My MR model has 64% identity to my unsolved protein. The crystal protein is 24kD and runs as a monomer or sometimes a dimer. Xtriage strongly suggests that there is tNCS due to a strong patterson peak at 0.5, 0.5. 0.5. Using the phaser GUI, when I search around P4, I get very promising statistics (TFZ = 20's and LLG ~2000), and oddly, in these cases phaser places two subunits on top of each other (despite default packing limitations) with the protein beta sheet cores overlapping, and rotated 180 degrees of each other. The density looks believable, but obviously something is very wrong. The crystal packing would be feasible if another subunit were placed, but I have been able to coax phaser to find a complete solution. It would rather place it overlapping than in available spaces. My questions: 1) does this suggest that there is some form of twinning going on? 2) sometimes phaser (phenix GUI) tells me it is adjusting for tNCS and sometimes it says its NOT (even when there is an even number of subunits being searched for), is this a bug or deliberate? 3) I have tried using phaser from the command line in MR_AUTO mode with the keywords TNCS_USE ON TNCS PATT PERCENT 88 TNCS_NMOL 2 or 4 but dont see any indication that the TNCS adjustments are being made and I have not been able to repeat my phaser GUI results this way. 4) What is a good strategy for tackling this particular problem? Right now I am just chugging through my list of possible space groups, compositions and resolution ranges, but need to look through each possible solution individually because of the misleading statistics and so is very inefficient and time consuming. Thank you for any help or comments. Ian

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Re: [phenixbb] Question about refinement group definition
by Shota Nakamura 21 Nov '12

21 Nov '12

中村昇太 Pavel Afonine <pafonine(a)lbl.gov>: >Hi Carsten, > >some keywords have type "multiple" and some not. In your example, >rigid_body has type multiple, that is you can specify as many of them as >you want: > >rigid_body = chain A >rigid_body = chain B >rigid_body = chain C > >and that means you will be refining three rigid bodies. Same applied to >tls, and many others. > >anisotropic is not multiple, so it can be only one. I recall I had >reasons to make it this way when implementing it but it was long long >time ago, so I forgot what it was. > >To see all attributes for all parameters: >phenix.refine --show-defaults=all.all > >which will yield a long hard to digest list. > >Pavel > >On 11/20/12 6:25 PM, Schubert, Carsten [JRDUS] wrote: >> Hello all, >> >> I have a question about the parameter definition for refinement groups (hope I picked the right term here). How does the definition and handling of refinement groups vary from the "refine.sites.rigid_body" scope to the "refine.adp.anisotropic" scope? For instance: >> >> refine { >> strategy = *individual_sites individual_sites_real_space *rigid_body \ >> *individual_adp group_adp tls *occupancies group_anomalous >> sites { >> individual = None >> torsion_angles = None >> rigid_body = chain A >> rigid_body = chain B >> } >> adp { >> individual { >> isotropic = None >> anisotropic = chain A >> anisotropic = chain B >> >> } >> >> would refine chains A and B as separate rigid groups, whereas only chain B would be refined anisotropically. >> Is this an intended behavior? >> >> BTW "anisotropic = chain A or chain B" refines both chains as expected. >> >> Cheers, >> >> Carsten >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb

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radiation damaged residues occupancy refinement
by Mikalai Lapkouski 20 Nov '12

20 Nov '12

Hello, I have a 1.2A model with the signs of radiation damage, judged by the negative peaks around the carboxyls (atoms CD, OE1 and OE2) of glutamates probably due to decarboxylation. I wan to refine occupancy of those atoms to account for negative density. What is the proper way of doing it? I tried to set the occupancy for those atoms 0.8 and refine individually. But obviously occupancies for those atoms are individually refined to different values which I dont think is the right way. Is there a way of how to refine occupancies for those atoms so that they remain identical after refinement (say all have 0.6)? Or is there another procedure of how to deal with refinement of radiation damaged side-chains? Any suggestions, please? Thank you Nick

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Job history recovery
by Damian Niegowski 20 Nov '12

20 Nov '12

Hello all, I have run into a problem with the Job History tab in the GUI. For one project there is a listing of 16 jobs but when I try going into Job History there is nothing. The .phenix directory for that project is present and all other directories of the individual jobs are there. Is there a way to "restore" the job history from existing parameter files? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegowski(a)ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39

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