[phenixbb] PHENIX 1.3 Available

Paul Adams PDAdams at lbl.gov
Sun Aug 17 16:35:59 PDT 2008

                              PHENIX 1.3 Release

The PHENIX developers are pleased to announce that the 1.3 general  
version of PHENIX is now available. Binary installers for Linux, and  
platforms are available at the download site:


This version of PHENIX includes tools for:

- Assessing data quality (phenix.xtriage)
   - Includes the detection of twinning, tNCS, and missed symmetries

- Automated structure solution (phenix.autosol)
   - Combines automated substructure solution (phenix.hyss) with phasing
     (Phaser/SOLVE), substructure completion, phase improvement  
     and fast initial model building (RESOLVE)

- Automated molecular replacement (phenix.automr)
   - Maximum likelihood molecular replacement with Phaser

- Automated protein and DNA/RNA model building/rebuilding  
   - Combines automated model building (RESOLVE), phase improvement  
     and structure refinement (phenix.refine)

- Automated ligand fitting (phenix.ligandfit)
   - Fitting a known ligand or screening against a library of the 200  
     common ligands

- Structure refinement (phenix.refine)
   - Maximum likelihood targets, simulated annealing, TLS, constrained
     occupancy refinement, f'/f'' refinement, water picking, anisotropic
     B-factor refinement, twinned refinement, automatic treatment of
     alternate conformations, and joint refinement against X-ray and  

- Generation of ligand coordinates and restraints (phenix.elbow/ 
   - Input formats include SMILES and PDB
   - Restraints can be manipulated with the phenix.reel GUI

Full documentation is available here:


There is a PHENIX bulletin board:


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

Direct questions and problem reports to the bulletin board or:

     help at phenix-online.org and bugs at 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  
the generous support of the members of the PHENIX Industrial Consortium.

                              PHENIX 1.3 Release

Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.

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