PHENIX 1.24.1 beta now available
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
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
This is a beta test version, and we therefore look forward to feedback
and bug reports from users. Please direct questions and problem
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
Version 1.24.1b of PHENIX includes:
Wizards (in the PHENIX GUI and from the command-line)
- automated structure solution (from processed data to a first map
and model) using HySS, SOLVE, RESOLVE, and phenix.refine.
- automated molecular replacement, using PHASER. Followed by
automated model rebuilding using the AutoBuild wizard.
- automated model building or rebuilding combined with structure
refinement, using RESOLVE and phenix.refine.
- 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.
- mmtbx.xtriage (comprehensive data quality assessment, including
- 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)
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).
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
- 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. |
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
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