[phenixbb] Phenix version 1.21 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site:

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

Highlights for the 1.21 version of Phenix include:

- Likelihood-based docking of models into cryo-EM maps.
    • Full support for structure determination with AlphaFold models.
    • New joint X-ray and neutron refinement algorithm.
    • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ.

Detailed changes are:

- Full support for structure determination with AlphaFold models in Phenix GUI
  - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences
  - Phenix AlphaFold server
  - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation
- Cryo-EM tools support ChimeraX visualization
- Cryo-EM density modification and anisotropic scaling display local resolution
- Tutorials available for automated structure determination with PredictAndBuild
- New em_placement and emplace_local tools
  - likelihood-based docking of models into cryo-EM maps
- MOPAC v22 is now distributed with Phenix
- Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ
  - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface
  - Defaults to MOPAC's PM6-D3H4
  - Higher level QM available via 3rd-party Orca package
- Restraints
  - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd
- Automated tests for programs in the Phenix GUI
- ERRASER no longer supported and removed from installation
- Remove rebuild_predicted_model (duplicated by predict_and_build)
- JSON output added to MolProbity structure validation scripts

Please note that this 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 funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium.

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Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) 
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) 
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) 
Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) 
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) 

Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul 
ORCID: 0000-0001-9333-8219

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.

Executive Assistant: Michael Espinosa [ MEEspinosa at lbl.gov ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ AshleyDawn at lbl.gov ][ 1-510-486-5455 ]
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