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PHENIX 1.24.1 beta now available

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  • Paul Adams
    ======================================================================= PHENIX 1.24.1 Beta Release
    Message 1 of 2 , Jul 5, 2006
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      PHENIX 1.24.1 Beta Release

      On behalf of the PHENIX development team I am happy to announce that
      the next general release version of PHENIX is now available. Binary
      installers for Linux, SGI and Tru64 platforms are available at our
      download site:


      Current users of PHENIX should upgrade to this most recent release
      version. To obtain download instructions visit:


      Documentation for PHENIX is available at:


      There is a PHENIX mailing list at:


      There is a PHENIX wiki at:


      Please consult the installer README file or online documentation for
      installation instructions.

      This is a beta test version, and we therefore look forward to feedback
      and bug reports from users. Please direct questions and problem
      reports to:

      help@... and bugs@...

      Commercial users interested in obtaining access to PHENIX should visit
      the PHENIX website for information about the PHENIX Industrial


      This version of PHENIX has three main user interfaces: command-line
      tools, strategies and wizards. Wizards are available under the Wizard
      tab in the PHENIX GUI, and are designed to complete a complex
      structure determination process, making automatic decisions when
      possible, but prompting the user for additional information when
      necessary. Strategies are available under the Strategy tab in the
      PHENIX GUI, and are networks of tasks constructed to perform
      higher-level functions.

      Version 1.24.1b of PHENIX includes:

      Wizards (in the PHENIX GUI and from the command-line)

      - AutoSol
      - automated structure solution (from processed data to a first map
      and model) using HySS, SOLVE, RESOLVE, and phenix.refine.
      - AutoMR
      - automated molecular replacement, using PHASER. Followed by
      automated model rebuilding using the AutoBuild wizard.
      - AutoBuild
      - automated model building or rebuilding combined with structure
      refinement, using RESOLVE and phenix.refine.
      - AutoLig
      - automated ligand fitting into difference density maps using
      RESOLVE once a complete protein model is available.

      Strategies (in the PHENIX GUI)

      - Ligand screening against the top 200 ligands in the PDB, using
      - Structure solution (MAD/SAD and SIR(AS)/MIR(AS)) combining HySS,
      SOLVE and RESOLVE.
      - Phase improvement using maximum likelihood methods in RESOLVE.
      - Model building using TEXTAL or RESOLVE.

      Command-line tools

      - mmtbx.xtriage (comprehensive data quality assessment, including
      twin analysis)
      - iotbx.reflection_statistics (analysis of diffraction data)
      - mmtbx.fest (FA value calculation)
      - phenix.hyss (anomalous substructure determination)
      - textal.build (automated model building with TEXTAL)
      - elbow.builder (generation of ligand coordinates and restraints)
      - phenix.refine (automated structure refinement)
      - phenix.geometry_minimization (regularize a structure)
      - phenix.solve (solve)
      - phenix.resolve (resolve)
      - phenix.resolve_pattern (resolve_pattern)
      - iotbx.mtz.dump (write useful information about a MTZ file)
      - iotbx.pdb.hierarchy (write useful information about a PDB file)

      Citing PHENIX

      If you use PHENIX for solving a structure please cite this

      PHENIX: building new software for automated crystallographic structure
      determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung,
      T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini,
      N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002).

      PHENIX Developers

      Lawrence Berkeley National Laboratory

      - Paul D. Adams
      - Pavel Afonine
      - Ralf W. Grosse-Kunstleve
      - Nigel W. Moriarty
      - Nicholas K. Sauter
      - Peter H. Zwart

      Los Alamos National Laboratory

      - Tom C. Terwilliger
      - Li-Wei Hung
      - Thiru Radhakannan

      University of Cambridge

      - Randy J. Read
      - Airlie J. McCoy
      - Laurent C. Storoni

      Texas A&M University

      - Jim C. Sacchettini
      - Tom R. Ioerger
      - Kresha Gopal
      - Lalji Kanbi
      - Erik McKee
      - Reetal K. Pai
      - Tod D. Romo
      - Jacob N. Smith


      We are very grateful to the following for making code or libraries
      available to us:

      - Alexei Vagin and Garib Murshudov for the CCP4 Monomer Library.
      - The CCP4 developers for making the MTZ library available to us.
      - Kevin Cowtan for contributing to the cctbx reciprocal space
      asymmetric units.
      - David Abrahams for developing the Boost.Python library.


      The development of PHENIX is principally funded through the Protein
      Structure Initiative of the National Institute of General Medical
      Sciences (NIH) under grant P01GM063210. For further information about
      the Protein Structure Initiative please visit:


      We also acknowledge the generous support of the members of the PHENIX
      Industrial Consortium. For more details please visit:


      PHENIX 1.24.1 Beta Release

      | Paul Adams, |
      | Senior Staff Scientist, Physical Biosciences Division |
      | Head, Berkeley Center for Structural Biology |
      | Deputy PI, Berkeley Structural Genomics Center |
      | Building 64, Room 248 | Lawrence Berkeley Laboratory, |
      | Tel: 510-486-4225 | 1 Cyclotron Road, |
      | FAX: 510-486-5909 | BLDG 64R0121, |
      | mailto:PDAdams@... | Berkeley, CA 94720, USA. |
    • Lukacs, Christine
      Hi- I have a bromine in my ligand, and it always refines with a much higher b-factor than the rest of the ligand, and correspondingly, a bunch of negative
      Message 2 of 2 , Jun 17, 2009
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        I have a bromine in my ligand, and it always refines with a much higher b-factor than the rest of the ligand, and correspondingly, a bunch of negative density and distorted b-factors for the adjacent atoms.

        I am wondering if the non-bonded term in my parameter file is way off. I am using xplo2d to generate my top/par files. The nonbonded term is:

        NONBonded BR 0.3200 3.884 0.3200 3.884

        Thanks -


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