[phenixbb] Phenix version 1.19 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.19 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site:

	http://phenix-online.org/download/

Please note that this recent publication should now be used to cite the use of Phenix:

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471

Highlights for the 1.19 version of Phenix:

- phenix.real_space_refine:
  - Improved rotamer fitting (use multiprocessing, in case of NCS constraints
    work on one copy only and propagate changes to all related copies, various
    performance improvements and bug fixes)
  - Improved map/restraints weight calculation
  - Morphing can now use multiprocessing (nproc)

- phenix.map_to_model and phenix.trace_and_build
  - Improved high-resolution model-building including detection of insertions
    and deletions 

- New methods 
  - phenix.local_resolution: calculates a local resolution map
  - phenix.local_aniso_sharpen: optimizes a map taking into account local
      resolution-dependence and anisotropy of the map and its errors

- New scripting tools
  - High-level scriptable Python tools are now available for map and model 
     analyses and manipulation as well as for model-building

- Restraints
  - Adjusting the "positions" of atom names in (pseudo-)symmetric amino acid
    side chains is now the default
  - Improved restraints for ARG allows more flexibility of the CD atom

- Bug fixes
  - Chains with modified amino or nucleic acids can be aligned
  - Fixed handling of modified amino/nucleic acids in sequence alignment


For a full list of changes see:

	http://www.phenix-online.org/documentation/CHANGES

Please note that this new publication should be used to cite the use of Phenix:

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471

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 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 acknowledge
the generous support of the members of the Phenix Industrial Consortium.

--
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib)
Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov)
Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu)
Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu)

Building 33, Room 250
Building 978, Room 4126
Building 977, Room 180C
Tel: 1-510-486-4225
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Ashley Dawn [ ashleydawn at lbl.gov ][ 1-510-486-5455 ]
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