- phenixbb - phenix-online.org

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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No bonded contacts
by Mark Saper 10 May '14

10 May '14

Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file. Thanks. Mark

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Rosetta_refine stuck...?
by Jan Gebauer 10 May '14

10 May '14

Hello everyone, First of all thanks to the developers for improving the installation of rosetta_refine. In contrast to my experiences half a year ago, this time the installation was easy and straightforward. However, refining a 600 Aa @ 3.5 A with 4 mol per asu one more than one processor still completely breaks my computer. (Intel i5 2500K / 7.8 GB RAM) I think this might be a memory issue. Having only a "normal" PC, one process already uses 5GB of RAM which equals 60% of my RAM. With only one process running the first of five model was finished in roughly 3 hours. However, the second model already takes more than 10 hours, and the log file on the _ros_tempXXX file wasn't update for the last 9 hours. I can't see any progress, however it still uses 100% of one processor. Unix's top tells me that "reduce" is completely using this resource and that it had run for the last 821 minutes... so I guess rosetta_refine is somehow stuck? Any ideas why it is stuck and how to solve that? With kind regards, Jan Gebauer By the way: Is rosetta_refine meant to work on a "normal" Computer - like mine. In principle I would have access to a cluster, but set-up time there would be considerably long for me... -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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FEM mtz won't open in coot
by de Waal, Parker 09 May '14

09 May '14

Hello Everyone, I'm having trouble opening the map file generated by phenix.fem in coot. Each time I try and load the .mtz file the follow error occurs 'Failed to find any suitable F/phi columns in the MTZ file'. Dumping the mtz file I can see: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE 0 33 0 100.00 12.1 12.1 114.15 3.31 H H 2 NONE 0 33 0 100.00 12.8 12.8 114.15 3.31 H K 3 NONE 0 137 0 100.00 51.4 51.4 114.15 3.31 H L 4 NONE 0.0 10551.1 22963 71.24 406.13 406.13 39.60 3.31 F 2mFoDFc 5 NONE -180.0 180.0 22963 71.24 0.98 89.81 39.60 3.31 P PHI2mFoDFc 6 NONE 5.2 51589.8 0 100.00 1602.72 1602.72 114.15 3.31 F FEM 7 NONE -180.0 180.0 0 100.00 0.32 89.74 114.15 3.31 P PHIFEM If someone could help me to rename these columns to a coot friendly format so that I would be greatly appreciative. Best, Parker

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PHENIX.apply_ncs question
by Sun Bingfa 08 May '14

08 May '14

Hi guys, I've been working on a structure using NCS. When I run the phenix.apply_ncs to generate the whole structure using the original one chain PDB, it gave me a PDB with same atom number on the other chain. For example, I start with chain A and end in chain A and B (B is generated by NCS), while the atom number on chain B is just a duplicate of chain A, starting from 1. This cause error in the subsequent refinement trials. I'm wondering what program can correct this issue. Thanks, Bingfa

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PHENIX-Coot problem
by Marcelo Carlos Sousa 08 May '14

08 May '14

I recently updated to CCP4 6.4 including Coot. I updated the path in phenix to point to the coot wrapper startup script. Phenix then correctly starts Coot and both programs are "connected". However regularizations or real space refinement fail with the "Failed to find restraints for: …" message as if the dictionaries are not loading. This does not happen when starting Coot from the terminal or form CCP4i… Any ideas on how to solve this problem? ____________________________________________ Marcelo C. Sousa, Ph.D. Associate Professor Department of Chemistry and Biochemistry University of Colorado at Boulder 596 UCB Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 8425

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Making beautiful crystallographic maps with FEM (Feature Enhanced Map) - new Phenix tool
by Pavel Afonine 07 May '14

07 May '14

Dear Phenix users, this is a quick announcement of a new Phenix tool to improve crystallographic maps. Link below provides most information: from method overview and examples to usage details: http://www.phenix-online.org/presentations/fem_06MAY2014.pdf Should you have any questions, bug reports or any other feedback *please send it to me directly*. All the best, Pavel

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LAST DAY TO REGISTER: SBGrid/NE-CAT Computing School
by Michelle Ottaviano 07 May '14

07 May '14

We're in the final stages of planning for our June Computing School and *registration will close on Friday. *Join us in June for our data processing workshop followed by Phenix and Schrodinger/BioLuminate workshops. *Register Here <http://www.events.harvard.edu/profile/web/index.cfm?PKWebId=0x12902a67d>: Deadline Friday, May 9th* *Quo Vadis Structural Biology 2014* SBGrid/NE-CAT Computing School June 5-7, 2014 Harvard Medical School -- Boston, MA *Data Processing in Crystallography - June 5-6:* Speakers: Kay Diederichs, Phil Evans, Zbyszek Otwinowski, Jim Pflugrath, Dominika Borek, Piotr Sliz, Matt Benning, , Frank Murphy, David Neau, K. Rajashankar, Nick Sauter, Jon Schuermann, Clemens Schulze-Briese *Advances in Structure Determination with Phenix - June 7:* Paul Adams & Nathaniel Echols, Lawrence Berkeley National Laboratory Tom Terwilliger, Los Alamos National Laboratory *Improved Structural Modeling Using BioLuminate - June 7: * Melissa Landon, Ph.D., Schrodinger, Inc. Complete meeting details can be found here: https://sbgrid.org/news/sbgridne-cat-computing-school

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Occupancy refinement troubles
by Kieft, Jeffrey 07 May '14

07 May '14

Hello All, Question about occupancy refinement. I'm refining an RNA structure at 2.0 Angstrom resolution with bound ligands iridium hexammine and spermine. The location of the former can be confirmed in an anomalous difference map, but they are likely not full occupancy...likewise the spermine is likely less than one. When I use occupancy refinement, it leaves the RNA at full occupancy as expected, but refines each atom of the irhex and spermine individually, in some cases driving the occupancy to 0 for some atoms. It seems like this was an issue in the past, but I'm still seeing it. Any ideas? Could if be that Phenix doesn't recognize those ligands? Parameter files wrong? Thanks for help! Jeff

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Current version download
by Marcelo Carlos Sousa 07 May '14

07 May '14

I was checking for the current official Phenix release and the website lists 1.9-16090. However, upon downloading it seems to be 1.8.4-1496… Am I doing something silly? Marcelo

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Geometry regularization in phenix.pdbtools
by Francis Reyes 06 May '14

06 May '14

Hi all, I always enjoyed geometry regularization in phenix.pdbtools. Has it been moved elsewhere? phenix.pdbtools file.pdb --geometry-regularization ceases to exist . Thanks, F

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Phenix-rosetta refinement problems
by Oliver Clarke 05 May '14

05 May '14

Hi all, I am struggling a little to get Rosetta and phenix to play happily with one another (I’d like to use the phenix.rosetta_refine module). I am currently using the latest nightlies of phenix (1.9-1690) and rosetta (2014.16.56682), and I run into errors (reproduced below) when attempting to build the phenix-rosetta interface. Does anyone have any insights as to how to fix this problem, or suggestions as to which pair of phenix and rosetta versions are known to be compatible with one another? Many thanks, Oliver. Errors while building phenix-rosetta interface: <snip> chdir(tempdir_.c_str()); src/core/scoring/cryst/PhenixInterface.cc:375:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::string)': src/core/scoring/cryst/PhenixInterface.cc:949:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1075:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1095:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1104:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ g++ -o build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/MinimizationGraph.os -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/MinimizationGraph.cc cc1plus: all warnings being treated as errors scons: *** [build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors.

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Post Doctoral Positions in Membrane Protein Structure and Function at the National Institutes of Health (NIH)
by Anirban Banerjee 03 May '14

03 May '14

Dear all, Please circulate to those who may be interested - The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We will combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based biochemistry, electrophysiology together with synthetic chemistry to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH. The DC Metro area is a wonderful place to live, the weather is pleasant and is a vibrant international community. In terms of scientific opportunities, the NIH is absolutely unique in bringing scientists from a virtually all corner of biomedical sciences in one campus. The Cell Biology and Metabolism program is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The candidates should hold a Ph. D. degree, must be motivated and a have strong background in biochemistry or structural biology. Experience with protein expression, purification and biochemical characterization is required. Prior experience in membrane protein biochemistry or insect/mammalian expression systems will be added advantages. Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. Disclaimers: The NIH is dedicated to building a diverse community in its training and employment programs and this position is subject to a background investigation. Thanks very much. Best, Anirban

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Partial Model for Mol Rep.
by Yuri 02 May '14

02 May '14

Hi Everyone, I am trying to solve a structure (to 2.15 Ang). I am pretty sure about one of the domains fold but it only covers residues 26-250 while the whole protein is 470aa. Could I attempt to use this small part of the protein to phase my data and hopefully start building? How is that handled in PHENIX? ps. Selenomet protein will be expressed soon.. -- Yuri Pompeu, Ph.D.

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refining two chains into same density
by Scott Horowitz 02 May '14

02 May '14

I have a strange case where I think there are two separate protein chains that are partially occupying the same spot (i.e. two proteins:one binding site=half of each bound). I'd really like to try to simultaneously refine both chains at partial occupancy into this density, but when I tried this (not surprisingly) it terminated because there were some overlapping atomic coordinates between the two chains. Is there a way to work around this? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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phenix start-up error !
by abhisek Mondal 01 May '14

01 May '14

hi. I have recently installed phenix-1.8.4 in my lab's RHEL work-station using './install' command. When i try to use 'phenix command' , the cursor of the terminal goes on blinking for almost hours, before opening the gui. Is there any way to avoid such long start-up time.! thank you. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics* *Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

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problem with MR
by Subhani Bandara 30 Apr '14

30 Apr '14

Hi all, I am trying to solve the structure of 7 KDa protein with a cubic space group at 1.35A resolution with Phaser-MR. It gives the error massage saying "The composition you have entered has a protein/nucleic acid content of 300.3%, which is impossible. Decrease your composition" and stops. This appears even if I give one chain as search model and say there is only one component copy. How can I fix this. Thanks Subhani

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CASP 11: Call for targets to assess the state of the art in protein structure modeling
by Torsten Schwede 29 Apr '14

29 Apr '14

Summary: CASP is soliciting target proteins for structure prediction - specifically proteins with new folds, membrane proteins, disordered proteins, oligomers, complexes, and multi-domain proteins. Call for targets: ============= As many of you know, CASP (Critical Assessment of Structure Prediction) has been assessing the state of the art in modeling protein structure from sequence since 1994, running a community experiment once every two years. In these experiments, information on soon to be solved structures is collected from the experimental community, and the sequence data are passed to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. CASP is only possible because of the generous participation of the experimental community in providing the modeling targets (3). The prediction season for the next full biannual experiment, CASP 11, begins May 1, and so we are now asking for your help in reaching our goal of releasing at least varied 100 targets in a the three-month period. We need all sorts of targets, spanning the categories below: 1. (More than ever) novel folds and membrane protein targets. Even with the extended collection season provided by CASP ROLL, there will be still a shortage. There are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. Oligomers, complexes, and multi-domain proteins: This round, CASP has entered collaboration with CAPRI for specifically assessing the accuracy of predictions of protein-interactions and relative domain orientation. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. We are especially interested in targets where disorder has been directly characterized experimentally, e.g. by NMR. 4. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 5. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. Procedure ========= For those of you who have not provided targets to CASP before, the procedure is simple. There are three ways to submit targets: (1) Go the target submission web page and fill in the easy form; (2) When you submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, automatically setting up a target entry; (3) Send an email the prediction center with details. If you have queries, there is very experienced prediction center staff to deal with them. The key thing is timing: We need a window of at least four weeks between receiving information about a target and the release of your experimental structure. A longer window - up to eight weeks - is often useful, for example so that a target can be used to test refinement methods, but is not essential (note that using the PDB target submission route automatically selects eight weeks). We don't need your experimental structure in advance of its release by the PDB, provided that will happen by the end of August. Please consult the target submission page for more details: http://www.predictioncenter.org/casp11/targets_submission.cgi There are already many prediction teams signed for CASP 11, and so any targets provided will receive plenty of attention. If you have a suitable target now, we are ready to receive it. If new targets come up before mid of July, we would also love to have them. (After July, we will continue with CASP ROLL for novel folds, disordered proteins, and membrane proteins). So please get in touch whenever a suitable opportunity arises, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Anna Tramontano, University of Rome, Italy Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland References ========= 1. Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy; Schwede, Torsten; Tramontano, Anna (2014). Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins, 82(S2), 1-6. 2. Kryshtafovych A, Fidelis K, Moult J. (2014) CASP10 results compared to those of previous CASP experiments. Proteins. 82 (S2):164-174. 3. Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V; Craig, Timothy K; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C; van Raaij, Mark J; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10(th) Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins, 82(S2), 26-42. Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp11/ Submit a target: http://www.predictioncenter.org/casp11/targets_submission.cgi

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MRage problem
by Appu kumar 27 Apr '14

27 Apr '14

Hello all, I am trying to find the molecular replacement for a protein of 75kDa at 6.1A, Space group is I422. MRage gave me a good solution once. But when i repeated the MRage with same parameters, it is not giving me the same solution and giving me wrong solution. Would you please help me in getting the solution which i got once. I have the information about the euler anglle. I will be highly grateful for the help. Thank you Appu

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Low resolution refinement
by Appu kumar 26 Apr '14

26 Apr '14

Hello All, I want to refine the low resolution structure (6.5A). It is a membrane protein and we are able to phase it. It will be great help if any one can guide me how to proceed further with the refinement. People uses Phenix to refine low resolution structure, so phenix is really a good program to proceed for refinement against low resolution. Thank in advance Appu

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Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

Dear all, I would like to try phenix.rosetta_refine and it is said in the online tutorial that the phenix should be built from source code in linux. However I ran into some errors, and I am too far from a linux export to figure it out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the source installer (phenix-installer-1.9-1683-source.tar) and run the installer as: # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from README-DEV that there is no --python-shared flag as described in the online tutorial) After while, I receive the following error message: ************************************************************************************************************************* Installing Imaging... log file is /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log getting package Imaging-1.1.7.tar.gz... using /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz Traceback (most recent call last): File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", line 9, in <module> install_cctbx_base.installer(args=sys.argv, log=sys.stdout) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 95, in __init__ self.build_cctbx_dependencies() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 134, in build_cctbx_dependencies self.build_imaging() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 349, in build_imaging confirm_import_module="Image") File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 325, in build_python_module_simple log=pkg_log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 150, in call return call(args, log=log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", line 51, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python setup.py build ' failed with exit code 1 FATAL ERROR: aborting installation. ************************************************************************************************************************* I looked into Imaging_install_log, and at the end, I have the following errors: ************************************************************************************************************************* /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libpython2.7.a: could not read symbols: Bad value collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 *************************************************************************************************************************** Could anybody help me out? Thank you so much, Chen

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