- phenixbb - phenix-online.org

phenix.real_space_refine
by Gino Cingolani 16 May '14

16 May '14

Hi all, I'm trying to refine a pdb against an EM map using phenix.real_space_refine using default parameters (e.g. phenix.real_space_refine model1.pdb map.ccp4). The program starts OK but quickly stops with the following output (see below) Any thoughts? Thanks so much! Gino ########################################################################### Add C-beta restraints ********************* Adding C-beta torsion restraints... num c-beta restraints: 11832 ------------------------------------------------------------------------------- Getting target map ****************** Traceback (most recent call last): File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 494, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 273, in __init__ self.caller(func = self.get_target_map, prefix="Getting target map") File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 298, in caller func(prefix=prefix) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 372, in get_target_map number_of_macro_cycles = self.params.refinement.macro_cycles) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 153, in extract_target_map_data_and_crystal_gridding crystal_symmetry = inputs.xray_structure.crystal_symmetry()) File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map use_sg = True) File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based() AssertionError ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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NCS in mr_rosetta
by Stefan Knight 15 May '14

15 May '14

Hi, Is there some way to make mr_rosetta use information about NCS present in the data? I have data from a crystal in sg P21 with a clear 3-fold axis perpendicular to the two-fold screw (as seen in self rotation function), and most likely 6 molecules in the asymmetric unit, but none of the mr_rosetta solutions that have appeared so far show 3-fold symmetry, and it doesn’t seem like the ncs is used in the search. The only info about ncs in mr_rosetta I have been able to find online pertains to extracting NCS from search models or mr_rosetta assembled models. Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

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fem command/memory error
by Matteo Colombo 14 May '14

14 May '14

Hi Pavel, I downloaded the last released version of phenix (phenix-1.9-1692) and I would like to run the "feature enhanced map" command. However, when I run it I got the following Memory Error that I didn't have in the previous version of phenix. r_work: 0.1867 r_free: 0.2372 Max B subtracted from atoms and used to sharpen map: 20.0 b_sharp: 25.0 FEM loop: done so far: 10%Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 120, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 99, in run sharp=params.sharp, signal_threshold=params.signal_threshold) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 112, in __init__ progress_counter = progress_counter) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 204, in fem_loop weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 276, in fem_loop_ weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 234, in one_iteration m = get_map(mc=mc_wa, cg=crystal_gridding) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 20, in get_map fourier_coefficients = mc) File "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", line 4357, in __init__ conjugate_flag=True) MemoryError My OS is Ubuntu precise 12.04 LTS, system 32 bit Thanks in advance Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structural J. P. Ebel 6, rue Jules Horowitz F-38027 GRENOBLE Cedex 1

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Re: [phenixbb] Non bonded contacts
by Mark A Saper 14 May '14

14 May '14

Pavel, Your suggestion of setting the alt-loc the same for the two residues in order to avoid the non-bonded contact restraint is not working yet. Do the residues need to be in the same chain Thanks, Mark On May 12, 2014, at 12:23 PM, Mark A Saper <saper(a)umich.edu> wrote: > Hi Pavel, > > I'll try that. I have a PLP cofactor and a lysine. I refined with them forming a Schiff base but the maps had large delta F indicating that the PLP ring was being pulled out of density. So now I am modeling it as PLP and Lys. But there is some bridging density. I want to see how close the Lys would extend if it didn't see the PLP. > > Thanks, > Mark > > On May 9, 2014, at 8:25 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Mark, >> >>> Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file. Thanks. >> >> you can asigne them diferent altloc identifiers and then they will not see each other via non-bonded interactions. >> If these two residues in question are symmetry mates then there is a keyword for this: custom_nonbonded_symmetry_exclusions . >> >> Also, I wonder why you want to do this? >> >> Pavel >> >

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Using command-line Phenix from the Mac graphical installer
by Nathaniel Echols 13 May '14

13 May '14

A public service announcement: the graphical installer gives you access to all of the same tools as the command-line installer. The only differences are a) the location, and b) we remove some of the bulkier data files that are not required for normal operation. (Which means that the graphical installation is actually about 300MB smaller.) Instructions are here: https://www.phenix-online.org/version_docs/1.9-1692/install-setup-run.html#… In general, I recommend that all (64-bit) Mac users run the graphical installer unless you absolutely need Phenix to go somewhere other than /Applications. (I know that some of you are already aware of this, but I've had to make this same suggestion twice already today, and the command-line installer is more work to support, thank you Apple.) -Nat

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Phenix version 1.9 released
by Paul Adams 13 May '14

13 May '14

The Phenix developers are pleased to announce that version 1.9 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Significant changes to the content and presentation of documentation, major improvements to HySS and AutoSol for SAD phasing in cases of weak signal, new Phenix/Rosetta refinement program for difficult low resolution refinements, new real space refinement program for refinement against a density map (e.g. cryo-EM), feature enhanced maps (FEM) enhance weak features and reduce noise and bias, new composite omit map program, unified MolProbity validation program (consistent with the MolProbity web server), proximity restraints for group displacement parameter refinement in phenix refine, and option for automated chemical linking in phenix.refine. Graphical interface: ==================== - Rearranged main interface to accompany documentation changes - New Phenix releases may be downloaded directly from the GUI (requires previously registered academic email address or permanent user credentials) - Added command to remove large data files (.geo, .kin, .ccp4, etc.) from a project directory to conserve disk space - Changes to support Mac OS 10.9 ("Mavericks") General: ======== - Re-organized and updated documentation - Binary installers for Ubuntu (10.04 or later) available - Python built as shared library in Linux builds (facilitates Rosetta hybrid) - new commands: phenix.composite_omit_map, phenix.rosetta_refine, phenix.molprobity, phenix.sceds, phenix.fem, phenix.real_space_refine, and many smaller utilities Refinement: =========== - phenix.refine: - similarity restraints for group isotropic B-factor refinement - set by group_b_iso.use_restraints (default=True) - data/restraints targets weight is determined automatically; can be adjusted by setting group_b_iso.restraints_weight (larger value makes restraints stronger) - various rotamer handling bug fixes - Automatic linking generation in phenix.refine and other programs that require restraints can be requested using the parameters link_all=True - handles any appropriate ligand-protein or ligand-nucleic acid covalent bonds, including sugars, amino acid modifications, and other prosthetic groups - behavior can be adjusted by setting maximum bond distances parameters - added "bfactor" and "occupancy" keywords to atom selection syntax (also applies to phenix.pdbtools) - Integration with DivCon suite (http://www.quantumbioinc.com) for QM refinement of ligands (requires separate license and installation) - phenix.rosetta_refine (new command): - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.ensemble_refinement: - enabled use of experimental phases (MLHL target) - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.morph_model: - fixed serious bug present in versions 1449-1626 that resulted in incorrect offset being applied Experimental Phasing and Model Building: ======================================== - HySS (phenix.hyss): - Substructure search much more fully automated: - Search first with Patterson seeds and direct method - If no clear solution, try more seeds, Phaser completion, and varying resolution - Full parallelization makes the search rapid - AutoSol: - Now much more powerful for weak SAD data: - Incorporates new automated Hyss search - Classic solvent flipping density modification after Resolve density modification - Tests several values of smoothing radius for solvent boundary identifcation for weak data - Iterates heavy-atom substructure search with Phaser completion including density after density modification and using model after model-building - Require solutions scored by correlation to be substantially better than altermatives before eliminating alternatives - Building with helices_strands_only set as default for data at lower than 3 Angstroms - AutoSol, AutoBuild, and LigandFit: - You can now specify the value of the test set flag for the free data with test_flag_value=xxxx Molecular Replacement: ====================== - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.find_alt_orig_sym_mate: - offset the produced MLAD value with log(0.9) to avoid negative values if identical structures were to be compared. Consequently older versions therefore yield MLAD values which are 0.10536 smaller than the current version. New commands: ============= - phenix.rosetta_refine (new command): - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.molprobity (new command): - Unified validation tool for command-line users; similar to existing comprehensive validation in the Phenix GUI - optional output of script for viewing results in Coot, or kinemage file - phenix.composite_omit_map (new command): - Default method uses very fast iterative de-biasing procedure - Can also generate either a simple or composite omit map with refinement and optional simulated annealing - Will generate multiple map types at once - parallelizable on multi-core systems or managed clusters - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.fem (new command): - Compute "feature-enhanced" map ("FEM") - this protocol modifies a 2mFo-DFc sigmaA-weighted map such that the resulting map has strengthened weak signal, if present, and a reduced amount of noise and model bias. - combines randomization and averaging, treatment of missing reflections, residual composite omit map, and histogram equalization - resulting maps are more interpretable and have less bias compared to the starting 2mFo-DFc map - very fast procedure, no refinement required - phenix.map_to_structure_factors (new command): - convert map into structure factors (also intended for EM) - phenix.angle (new command): - compute angle between two axes or two atom selections - phenix.model_model_distances (new command): - Given two PDB files compute distances per atom, residue, chain, model and overall. It is assumed (and asserted in the code!) that the amount and order of atoms in both files are identical. - phenix.fab_elbow_angle (new command): - Calculating Fragment Antigen-Binding (Fab) elbow angle - phenix.f000 (new command): - Given PDB file estimate F(0,0,0); includes atomic model and bulk-solvent Ligands: ======== - phenix.ligand_identification: - Now you can use ligand cif files (in addition to .pdb files) to build your own custom ligand library. Just specify "Ligand directory" (GUI) or use keyword "ligand_dir" (command line) to tell the program to use .pdb or .cif files in your own ligand directory. - Bug fix to properly handle mtz labels when using difference maps. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Re: [phenixbb] HLs not recognised
by Nathaniel Echols 13 May '14

13 May '14

Here is the problem: phenix.mtz.dump resolve_1_190_phenix.mtz ... HLA xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLB xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLC xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLD xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) We ignore arrays with all zeros, since they're obviously not correct - however, the feedback given to the user is deficient. I am open to suggestions about how we can improve this, but I am reluctant to assault users with pop-ups every time bogus information is detected, especially since this will increase the latency of the GUI. The file from AutoSol you should actually use is probably named overall_best_refine_data.mtz, which contains the original, purely experimental phases (along with data and R-free flags, of course). We don't recommend using the density-modified phases as restraints. (I am not sure why Resolve would output all zeros; that is a question for Tom. I did however notice the same thing in a file generated by AutoSol for a tutorial dataset.) -Nat On Mon, May 12, 2014 at 8:21 AM, Jonathan Grimes <jonathan(a)strubi.ox.ac.uk>wrote: > > hi nat > > i created this mtz file.....by taking a resolve.mtz > and putting it back thru phenix. > > from the GUI and from the command line phenix > doesnt like my HLs coeffs. > > thanks > jon > > Dr. Jonathan M. Grimes, > NDM Senior Reseach Fellow Diamond Research > Fellow > University Research Lecturer Diamond Light > Source > Division of Structural Biology Diamond House > Wellcome Trust Centre for Human Genetics Harwell Science Campus > University of Oxford Didcot > Roosevelt Drive, OX11 0DE > Oxford OX3 7BN, UK > > Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 > > > > ---- Original message ---- > >Date: Mon, 12 May 2014 07:44:14 -0700 > >From: Nathaniel Echols <nechols(a)lbl.gov> > >Subject: Re: [phenixbb] HLs not recognised > >To: Jonathan Grimes <jonathan(a)strubi.ox.ac.uk> > >Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > This is a little strange - the GUI should not be > > allowing you to select an array that won't work for > > refinement. Could you please send me (off-list!) > > both MTZ files that you tried using? (I don't > > think I need data or anything else for this.) > > thanks, > > Nat > > > > On Mon, May 12, 2014 at 5:49 AM, Jonathan Grimes > > <jonathan(a)strubi.ox.ac.uk> wrote: > > > > i have now used phenix to read in the mtz file, > > read all the arrays > > and make a new mtz file. > > > > phenix recognised the HLs as Hend/latt coeffs. > > > > i used the eff file to run phenix.refine at the > > command line > > and got this error > > > > Not a suitable array of experimental phases: > > refinement.input.experimental_phases.labels=HLA,HLB,HLC,HL > > > > The phases were orginally derived by Phenix > > using the auto solve GUI. > > Jon > > > > Dr. Jonathan M. Grimes, > > NDM Senior Reseach Fellow > > Diamond Research Fellow > > University Research Lecturer > > Diamond Light Source > > Division of Structural Biology > > Diamond House > > Wellcome Trust Centre for Human Genetics > > Harwell Science Campus > > University of Oxford > > Didcot > > Roosevelt Drive, > > OX11 0DE > > Oxford OX3 7BN, UK > > > > Email: Jonathan(a)strubi.ox.ac.uk, Web: > > www.strubi.ox.ac.uk > > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - > > 287547 > > > > ---- Original message ---- > > >Date: Mon, 12 May 2014 11:32:39 +0100 > > >From: phenixbb-bounces(a)phenix-online.org (on > > behalf of Jonathan Grimes > > <jonathan(a)strubi.ox.ac.uk>) > > >Subject: [phenixbb] HLs not recognised > > >To: phenixbb(a)phenix-online.org > > > > > > > > > I am trying to refine a structure at low > > resolution and would like to > > > use phase restraints. using the GUI even > > though HLs are present > > > in the MTZ file, and are type > > “A”…checked with CAD…..i am not given > > > the option of selecting them. > > > > > > not clear to me what I’m doing wrong. > > > > > > hints most wellcome > > > thanks > > > jon > > > > > > > > >Dr. Jonathan M. Grimes, > > >NDM Senior Reseach Fellow > > >University Research Lecturer > > >DIAMOND Research Fellow > > > > > >Division of Structural Biology > > >Wellcome Trust Centre for Human Genetics > > >University of Oxford > > >Roosevelt Drive, > > >Oxford OX3 7BN, UK > > > > > >Email: Jonathan(a)strubi.ox.ac.uk, Web: > > www.strubi.ox.ac.uk > > >Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - > > 287547 > > > > > >_______________________________________________ > > >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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gui occupancy group selection crash
by Petri Kursula 13 May '14

13 May '14

Hi, I’m trying to set up constrained occupancy groups in the GUI, but trying to add selections, the entire Phenix GUI crashes. This happens when clicking the plus sign in the dialogue attached. This is with the PHENIX-1.9-1692 build (updating from 1.8.x did not help) with OSX Mavericks (10.9.2). I know this worked before smoothly, so there perhaps is a bug somewhere. Petri --- Petri Kursula, PhD project leader, adjunct professor Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg/DESY, Germany www.biochem.oulu.fi/kursula<http://www.biochem.oulu.fi/kursula> www.desy.de/~petri/research<http://www.desy.de/~petri/research> petri.kursula(a)oulu.fi<mailto:[email protected]> — [cid:9BE629E3-4781-4E71-BC21-2DB1CB2B9F59@localdomain]

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Continue mr_rosetta after system crash?
by Oliver Clarke 12 May '14

12 May '14

Hi all, I was running a mr_rosetta job on an 8-core machine, and after 3 days of apparently fruitful computation (784/1000 initial models generated), my system crashed for an apparently unrelated reason (there are no errors in the rosetta logs - I suspect a brief power outage or something of the sort). I am guessing the answer is no, but I just thought I’d check whether anyone knows of a way to continue such a job from where it left off without having to start from scratch? Best, Oliver.

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HLs not recognised
by Jonathan Grimes 12 May '14

12 May '14

I am trying to refine a structure at low resolution and would like to use phase restraints. using the GUI even though HLs are present in the MTZ file, and are type “A”…checked with CAD…..i am not given the option of selecting them. not clear to me what I’m doing wrong. hints most wellcome thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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