- phenixbb - phenix-online.org

Re: [phenixbb] metal coordination restrain on alternative conformation
by Zhang yu 08 Oct '13

08 Oct '13

Hi Nigel, Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation. Thanks Yu On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: > Thanks > > > On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > >> I ran >> >> phenix.metal_coordination >> >> and got the attached. Pass it to phenix.refine. >> >> >> On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: >> >>> Hi Nigel, >>> >>> Thanks. Please see attached PDB file. The structure has two molecules in >>> one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid >>> chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L, >>> M, N, O, P, Q, R, and S for molecule 2) >>> >>> There is only one nucleoside-triphosphate and its cognate MG++ in each >>> molecule having alternative conformations (named as conformation A and B). >>> The desired restrains are as follows, >>> >>> In molecule 1, >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain N and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> In molecule 2, >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain D and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> >>> >>> >>> >>> On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov>wrote: >>> >>>> Can you send the residues involved? >>>> >>>> Nigel >>>> >>>> NB. Any files sent to me will be held in strictest confidence. >>>> >>>> >>>> >>>> On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu <phenixzyfish(a)gmail.com>wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> My structure contains a metal coordinating to some residues, one of >>>>> which has alternative conformations. Phenix doesn't pickup the residue with >>>>> alternative conformation when I tried to generate metal restrains using >>>>> ready.set. >>>>> >>>>> Any idea? Thanks >>>>> >>>>> Yu >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>>>> >>>> >>>> >>>> -- >>>> 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 >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >> >> >> -- >> 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 >> > >

3 4

Refinement going wild in latest versions
by Hugues Nury 04 Oct '13

04 Oct '13

Hello everyone, I am experiencing differences with phenix.refine versions 1.8.3 or 1.8.4 compared to 1.8.2. Performing comparable runs, Rs are rising several percents with the latest versions, while marginally decreasing using version 1.8.2. I am a very recent convert to Phenix, so maybe I'm missing something obvious, but here are the details: Refinement strategy is xyz+real space+tls+individual Bs at 3.5 A, using NCS and secondary structure restraints, and weight optimization. Starting R/Rfree are around 24.5/28.5 Part of the problem seems to come from secondary structure restraints, with (many) messages in the log file of the refinement going wild looking like WARNING: could not process nonbonded pair Original error: cctbx Internal Error: /net/clover/scratch1/phenix/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/pair_tables.h(663): CCTBX_ASSERT(j_sym >= 0) failure. pdb=" N GLN B 130 " segid="B " pdb=" O VAL B 115 " segid="B " In log files of refinement with version 1.8.2, there are no such messages, and in either case the definition of beta strands were done automatically by Phenix But even secondary structure restraints are switched off, it starts ok but goes wrong at the beginning of cycle 2, during local real space refinement start: r_work=0.2271 r_free=0.2785 final: r_work=0.2418 r_free=0.2937 And then continue to worsen. Any help appreciated! Cheers, Hugues -- Hugues Nury Institut de Biologie Structurale 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France +33 6 52 45 17 79

3 3

REMARK 3 NCS
by Luca Pellegrini 03 Oct '13

03 Oct '13

Hello, I have noticed that Phenix 1.8.4-1496 (as well as 1.8.3-1479) appears to have stopped writing the REMARK 3 NCS in the PDB header. Is this so? It is useful to have that info when it comes to depositing the coordinates. Many 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

3 3

DEN refinement
by Jan van Agthoven 03 Oct '13

03 Oct '13

Hi everyone, I ran a DEN refinement of my low resolution structure (3.6) to improve my model. I typed in the following command: phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb reference.params with reference.params saying: refinement.reference_model.reference_group { reference = chain A and resseq 1:953 selection = chain A and resseq 1:953 } refinement.reference_model.reference_group { reference = chain B and resseq 1:687 selection = chain B and resseq 1:687 } because the reference file only contains chain A and chain B. Unfortunately I obtained much worse R factors then with a regular refinement: Start R-work = 0.2798, R-free = 0.3176 Final R-work = 0.3733, R-free = 0.4089 Does someone have an idea what could have go wrong? Thanks,

2 2

phaser error
by Alexander Batyuk 03 Oct '13

03 Oct '13

Dear developers, I'm getting the following error while running phaser: ERROR running main function (UNHANDLED): cctbx Error: Lattice type not specified. It comes when I put one placed model (found in a previous run) and search for another. Phenix version 1.8.4, on OSX 10.8.5 Do you have any suggestions? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

1 0

MR-SAD in phenix
by LISA 02 Oct '13

02 Oct '13

Hi All, If we have partial model we can run MR_SAD by adding a single new keyword to my AutoSol run: input_partpdb_file=MR.pdb But I only have a mtz file not a pdb file in the molecular replacement result with EM map as the model. How can I combine the EM result with SAD to improve the density? I have Ta6Br12 cluster soaked crystal data. How can I define the cluster? How much of F'' and F' of this cluster at the wavelength of 1.254A? Thank you. Lisa

2 1

Plotting disabled
by Luca Pellegrini 01 Oct '13

01 Oct '13

Hello, Phenix.refine (1.8.4-1496) disables plotting in the GUI, complaining that the libpng15.15.dylib is missing (see screen below). The library is actually there, where Phenix says it should be: /opt/X11/lib/libpng15.15.dylib. How do I get Phenix to load it? I am using Mac OSX 10.6.8. Many 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

2 1

metal coordination restrain on alternative conformation
by Zhang yu 01 Oct '13

01 Oct '13

Hi everyone, My structure contains a metal coordinating to some residues, one of which has alternative conformations. Phenix doesn't pickup the residue with alternative conformation when I tried to generate metal restrains using ready.set. Any idea? Thanks Yu

2 1

DEN refinement stuck
by Jan van Agthoven 25 Sep '13

25 Sep '13

Hi, I launched a DEN refinement 4 hours ago, and it remain stuck with the following message: ----------coordinate minimization before annealing---------- Running DEN torsion optimization on 1 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 3.0 Is this normal? Is torsion simulated annealing so long? Thanks,

2 2

Merging two or more dataset
by Singh, Bishal 24 Sep '13

24 Sep '13

Is it possible to merge two or more dataset of same protein of different crystals? If yes, please suggest me the way. I shall be grateful for your help. Bishal Singh PhD student University of Heidelberg, Germany

2 1

Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology (October 22, 2013) and PSI Workshop on Theoretical Model Archiving and Validation (October 21, 2013)
by Torsten Schwede 24 Sep '13

24 Sep '13

*Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology* Center For Integrative Proteomics Research Rutgers, The State University of New Jersey Tuesday October 22, 2013 http://www.proteinmodelportal.org/workshop-2013/ The wwPDB has established PDBx/mmCIF as the new standard format for data exchange and archiving in structural biology (http://www.wwpdb.org/news/news_2013.html#22-May-2013). To help facilitate the transition from PDB to PDBx/mmCIF format the wwPDB is organizing a programmer's workshop describing the content and organization of PDBx/mmCIF data, and the available software tools and libraries supporting PDBx/mmCIF (C/C++, Java, and Python). The workshop will be held on Tuesday, October 22, 2013 at Rutgers, The State University of New Jersey (in conjunction with a PSI Workshop on Theoretical Model Archiving and Validation to be held Monday, October 21, 2013): Starting at 9am, the morning session will include presentations from: Paul Adams (Phenix), David Case (AMBER), Tom Goddard (UCSF Chimera), Robert Hanson (JMol), Eugene Krissinel (CCP4/mmdb), Andreas Prilic (BioJava), John Westbrook (RCSB PDB). The afternoon session will offer an opportunity to work hands-on with the presenters and developers in the areas of structural biology and molecular modeling to learn application details and to discuss successful approaches and experiences in adapting software to support PDBx/mmCIF. In addition, the workshop will include a discussion of PDBx/mmCIF extensions required to represent molecular modeling specific information. There is no registration fee, but online registration is required (registration Deadline is October 4). For detailed agenda and online registration: http://www.proteinmodelportal.org/workshop-2013/ Looking forward to welcoming you at the workshop, Andrej Sali, John Westbrook, and Torsten Schwede ---- Prof. Dr. Torsten Schwede Biozentrum Universität Basel & SIB Swiss Institute of Bioinformatics Klingelbergstrasse 50-70 4056 Basel

1 0

define acetyl-methionine for coot and phenix
by Ursula Schulze-Gahmen 24 Sep '13

24 Sep '13

I am trying to include a N-terminal acetylated methionine in my model. I replaced my methionine with a AME residue from the pdb data bank and included a link command to connect the C from AME with the N of the second residue. The AME is defined as HETATM. When I try to regularize this structure in Coot it doesn't recognize that the 1. and 2. residue should stay connected. What or how do I need to define this residue or the connection so that I can model in Coot and refine in Phenix? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

3 6

Registration last day: "The Future of Microfocus Protein Crystallography"
by Marjolein Thunnissen 13 Sep '13

13 Sep '13

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

1 0

Research Assistant Position in Structural Biology of Macromolecular Complexes
by Sebastian Klinge 11 Sep '13

11 Sep '13

*Research Assistant Position in Structural Biology of Macromolecular Complexes* The Rockefeller University, a premier biomedical research institute, seeks a Research Assistant to join our Laboratory of Protein and Nucleic Acid Chemistry. The successful applicant will be part of a creative and highly motivated team of biochemists and structural biologists, which are interested in the structure and function of multi-protein complexes involved in key steps of the Central Dogma of Molecular Biology. The laboratory houses a state of the art large scale fermenter, tissue culture and crystallization rooms and has access to the Rockefeller Structural Biology Resource Center with liquid handling and crystallization robots (Formulator by Formulatrix and Phoenix by Art Robbins respectively) and a Rigaku/MSC microMax 007 HF X-ray generator. B.S. or M.S. degree with a strong background in biochemistry or molecular biology is required. Experience with protein production in insect cells (preferably MultiBac) and familiarity with molecular biology techniques is essential. The ideal candidate will interact well with other members of the laboratory, be well organized and interested in working in a high quality research environment and collaborate closely with the principal investigator in running the laboratory. Responsibilities will include setting up an insect cell facility as well as general laboratory duties such as inventory, organization and pick-up of supplies and cataloging the laboratory's clone stocks. We offer a competitive salary, comprehensive benefits, and a beautiful working environment. To apply to this job, click the following URL, click on 'staff opportunities' and enter keyword 'IRC14241': http://www.rockefeller.edu/hr/career /The Rockefeller University is an Affirmative Action/Equal Employment Opportunity/VEVRAA employer./

1 0

Autobuild
by Heather L Condurso 07 Sep '13

07 Sep '13

I'm a bit confused about what is going on with my autobuild run. I solved a structure from anomalous data to 2.7A but many loops are missing. I ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. I used mostly the default settings and rebuild_in_place=False. After a pretty short time I realized the run was over and at the bottom of the log I see this: Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 Deciding if we should continue... Recent R change per cycle: 0.0 Ending these build cycles as the recent change in R per cycle has been 0.0 and the required value of change is -0.005 and the R is somewhat acceptable at 0.276670644792 All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 All omit/non-omit regions completed finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 Finishing AutoBuild Run 162 Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat AutoBuild Run 162 Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz Sequence file: /Users/heather/Desktop/M/m.pir Best solution on cycle: 2 R/Rfree=0.26/0.33 Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb --- Model (CIF file) --- cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif --- Refinement log file --- log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine --- Model-building log file --- log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log --- Model-map correlation log file --- log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz You might consider making one very good model now with: phenix.autobuild \ data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \ model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ rebuild_in_place=True \ seq_file=/Users/heather/Desktop/M/m.pir My full sequence is 325 amino acids so only about 75% is build in. I am hoping autobuild can help find at least some of these missing residues. Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? I tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. Is this the best that autobuild can do? I also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. I appreciate any advice on how best to proceed. I am using 1.8.2-1472 if that matters. Thanks, Heather

2 3

Postdoctoral Researcher Opportunity in the application of free-electron lasers to structural biology.
by Edward Snell 06 Sep '13

06 Sep '13

Postdoctoral Researcher in application of free-electron lasers to structural biology. Open from Sept 2013 until filled. Employer: Hauptman Woodward Medical Research Institute (Position is situated in Germany) Outline of Position: This position is supported by a new NSF grant devoted to the application of free-electron X-ray lasers to structural biology. The position will be based in Hamburg, Germany at DESY CFEL, but is supported by a grant at SUNY Buffalo. There will be time for research collaborations in addition to support duties. The ideal candidate will hold a PhD in experimental Biophysics or similar. Major Responsibilities: 1) Application of X-ray free electron laser to structural biology and development of sample-delivery devices. 2) International travel to annual meetings being held in the U.S. 3) Collaboration with partner institutions and labs in the U.S. 4) Interact via web conferencing with the principal investigator and scientific director of the project Please send resume and cover letter to: Jill Szczesek Director of Operations and Academic Affairs Hauptman Woodward Medical Research Institute 700 Ellicott Street Buffalo, New York 14203 phone: 716-898-8597 email: jszczesek(a)hwi.buffalo.edu<mailto:[email protected]> Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Senior Scientist, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!

1 0

PDBTools and TLS
by Mark Saper 03 Sep '13

03 Sep '13

Hi, I couldn't find the answers to these questions in the documentation. 1. If I am refining TLS and individual isotropic ADPs, does phenix.refine derive iso-ADP from the ANISOU records presently in the file, or does it use the iso-ADP from the ATOM record and recombine it with the TLS values? 2. Consequently if I reset the B's for a range of residues on the ATOM cards only, will they be used rather than the ANISOU record to derive the ADP? Is it better to use PDBTools, specify the iso-ADP and also convert to ANISOU? I am doing this for only a selection of the residues. 3. Should phenix.refine input files retain the header lines containing the previously cycle TLS parameters? If so PDB Tools doesn't save them. PDB Editor does. Which is the preferred tool? 4. If one explicitly changes atom ADPs with Coot using Measures>Residue info... the output file reflects the change only in the ATOM lines, but the ANISOU line retains the previous 6 parameters. It seems as if coot should also change the ANISOU to reflect anisou (last 3 parameters=0). Comments or answers? Many thanks in advance! -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

2 1

Error determining reference matches
by Dan McNamara 31 Aug '13

31 Aug '13

Hi all, I am encountering a strange crash when running phenix.refine through the command line with reference model restraints turned on. The references point to two different PDB files, one labeled as chain A and one labeled as chain B. This error occurs whether I have my refinement model in P1 with 192 chains or P2(1) with 96 chains. The chains are A-EZ (192) or A-BH (96). It appears to fail to align the reference models to the sequences in the refinement model. This error does not occur with other smaller target structures under 25 chains and reference models used with the same installation of phenix. I am hoping for any advice on why this might be happening or how I might get around it. ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (401472 atoms) torsion_angles = False (0 atoms) rigid_body = True (401472 atoms in 192 groups) individual_adp = False (iso = 0 aniso = 0) group_adp = True (201984 atoms in 25824 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False n_use = 401472 n_use_u_iso = 401472 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 401472 *** Adding Reference Model Restraints *** determining reference matches automatically... Traceback (most recent call last): File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/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 "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/command_line.py", line 92, in run master_params=customized_master_params) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/driver.py", line 501, in __init__ log=self.log) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 147, in __init__ self.get_reference_dihedral_proxies() File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 460, in get_reference_dihedral_proxies log=self.log) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 323, in process_reference_groups moving_chain = mod_h) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/utils.py", line 426, in _ssm_align ssm_alignment = ccp4io_adaptbx.SSMAlignment.residue_groups(match=ssm) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 215, in residue_groups return cls( match = match, indexer = indexer ) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 176, in __init__ self.pairs.append( ( get( f, indexer1 ), get( s, indexer2 ) ) ) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 173, in get assert identifier in indexer, "Id %s missing" % str( identifier ) AssertionError: Id ('A', 1, ' ') missing Best, Dan

3 2

coot and mtz interpretation
by Heather L Condurso 31 Aug '13

31 Aug '13

I'm having an issue that when I launch coot from the phenix refine gui it loads the pdb and mtz fine, but the FoFc map colors are green and royal blue. When I open coot first and then load the pdb and mtz files, the FoFc map colors are green and red, but the blobs that were green in the phenix loaded maps are now red and what was royal blue is now green. Has anyone else had this issue? I am running a mac with OS X 10.6.8 and coot 0.6.1 and phenix 1.8.2-1309. I have an identical mac running all the same versions and everything loads green and red as expected. Is there a parameter file somewhere that tells coot how to display the phenix maps that may provide a clue as to what is going on? I appreciate any suggestions, Heather

3 4

a question on NAG-ASN cif file
by fn1＠rice.edu 30 Aug '13

30 Aug '13

Hi Nigel, I tried your nag_asn.cif file. I did not include hydrogen in the refinement, so i always get the error message that NAG-ASN could not be applied. So i remark the angle definition that contains hydrogen and the same for the plane definition, as follows, #NAG-ASN 1 C1 2 ND2 2 HD2 119.000 3.000 #NAG-ASN plane1 2 HD21 .020 by doing this, the program could run through. However, when i check the geometry output .geo file, only the added plane information is seen, no chirality of C1 in NAG is seen. Did i do something wrong? Thank you! Fengyun

2 1

a question on NAG-ASN cif file
by fn1＠rice.edu 29 Aug '13

29 Aug '13

Hi everyone, I am refining a glycoprotein model, and I have applied NAG-ASN link to the ASN. But the beta-conformation of NAG could not be retained after refinement for some sites. I read the cif file and find that there are only angle definitions for NAG-ASN. The dihedral and charility information are missing. Is there a way that I could retain the charility of C1 of NAG? Thank you! Fengyun

3 3

ALS Call for General User Proposals - DEADLINE SEPTEMBER 4 , 2013
by Banumathi Sankaran 29 Aug '13

29 Aug '13

> > The deadline for Jan/July 2014 Collaborative > Crystallography proposals will be *Sep 4, 2013. * > > ---------------------------------------------------------------------------------------- > Through the Collaborative Crystallography Program (CC) at the > Advanced Light Source (ALS), scientists can send protein crystals > to Berkeley Center for Structural Biology (BCSB) staff researchers > for data collection and analysis. The CC Program can provide a > number of benefits to researchers: > > * Obtain high quality data and analysis through collaborating with > expert beamline > researchers; > * Rapid turn around on projects; and > * Reduced travel costs. > > To apply, please submit a proposal through the ALS General User > proposal review process for beamtime allocation. Proposals are > reviewed and ranked by the Proposal Study Panel, and beamtime is > allocated accordingly. BCSB staff schedule the CC projects on > Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only > non-proprietary projects will be accepted. As a condition of > participation, BCSB staff researchers who participate in data > collection and/or analysis must be appropriately acknowledged - > typically being included as authors on publications and in PDB > depositions. Please consult the website for additional information at: > > http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography > > ----------------------------------------------------------------------------------------- > > > How To Apply: > > Please follow the instructions for proposal submission at: > http://www-als.lbl.gov/index.php/user-information/user-guide/58.html > Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" > and click on "New Proposal." Enter your proposal information. > > > > Regards, > Banumathi Sankaran >

1 0

processor usage controlin DEN
by miyatake 25 Aug '13

25 Aug '13

Dear phenixbb, Hello, I run DEN refinements using GUI (dev-1439). I wonder whether I can control the number of the processor used during the DEN refinement. I know that we can use nproc in command line, but I'd like use it in GUI. Best regards, H. Miyatake

2 4

phenix.real_space_refine
by Heather L Condurso 23 Aug '13

23 Aug '13

I tried to run the phenix.real_space_refine that was discussed in the CCN but I get the following error. import mmtbx.refinement.real_space.driver ImportError: No module named driver I downloaded the latest nightly build dev-1463. Even when asking for the help I get the same error. I did however successfully create some FEMs which look lovely. Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

3 3

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

23 Aug '13

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

1 0

Find peaks and holes documentation
by Morten Grøftehauge 23 Aug '13

23 Aug '13

Hi, I wanted to try phenix.find_peaks_holes with anomalous structure factors from XPREP but I ran into a few problems. And then I tried to fix them by reading the manual and that was really hard too. So first the missing manual. If I google it I get this page http://www.phenix-online.org/documentation/find_peaks_holes.htm which is for the GUI. When I go back to the documentation http://www.phenix-online.org/documentation/phenix_documentation.html I can't find the link for it (which is also why I was using Google to find it in the first place). I also checked the source to see if the link was somehow misnamed. Anyway, running it from the command line with default settings is not hard. phenix.find_peaks_holes model.pdb reflections.hkl but I run into this error message Sorry: Unresolved amplitude/intensity ambiguity: /path/path/path/reflections.hkl SHELX reflection files may contain amplitudes or intensities. Please append =amplitudes or =hklf3 or =intensities or =hklf4 to the file name argument or parameter to resolve the ambiguity. and I don't how to do that. If I add .hklf3 at the end of the file name I get the same error. If I go reflections.hkl=hklf3 I just get a message that I need to supply a reflection file. What is the syntax? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

2 4

coot add residue issue
by Heather L Condurso 21 Aug '13

21 Aug '13

Dear all, I have been trying to add a residue to my model in coot for hours now. The add terminal residue function adds a residue far from the end of my chain and I've tried moving it manually and it keeps going back and it never makes a bond between the two amino acids. Is there a trick in coot or a better way to do this in phenix? Thanks, Heather Condurso UF-Department of Chemistry

5 5

peptide ligand refinement problems
by Mengbin Chen 21 Aug '13

21 Aug '13

Dear Phenix Users, My colleague has got into trouble when he was refining a peptide ligand with a coumarin ring attached via a peptide bond. The peptide part is composed of natural amino acids, which does not require a cif file. On the other hand, a cif file has been created for the coumarin ring. Unfortuantely, after the refinement run, the peptide and the coumarin ring fell apart, and we could not figure out why this is happening. We are using the Phenix-dev-1370 version. Any help would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

2 4

Re: [phenixbb] HKL2000 behaved weirdly
by Mengbin Chen 21 Aug '13

21 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

1 0

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

3 2

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

3 2

Ensemble refinement, starting water structure and alternative conformations
by Joseph Noel 20 Aug '13

20 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 ______________________________________________________________________________________

2 1

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

3 2

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

2 1

problem with refinement in AutoBuild
by Michael Thompson 16 Aug '13

16 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

2 1

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

13 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

3 3

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

2 1

is phenix trying to polymerize b-octyl glucoside?
by Edward A. Berry 10 Aug '13

10 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

2 2

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 ______________________________________________________________________________________

1 0

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

3 2

MR Rosetta Error
by Masaki UNNO 06 Aug '13

06 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 1

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

3 2

How does phenix handle deuterium atoms in neutron diffraction data?
by Javier Gonzalez 03 Aug '13

03 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)

2 1

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]>

2 1

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]>

1 0

July 2013 Computational Crystallography Newsletter
by Nigel Moriarty 02 Aug '13

02 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

1 0

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

4 9

phenix-refine crash
by Carlos Frazao 01 Aug '13

01 Aug '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

3 2

distance threshold for special positions?
by Alastair Fyfe 01 Aug '13

01 Aug '13

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

2 1

proteins sequence for phenix
by LISA 27 Jul '13

27 Jul '13

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

3 2