For anyone who is confused:
Unfortunately, the link given here (https://phenix-online.org/download/) says
that the latest release is 1.19.2-4158! That’s very odd because the same URL
without the trailing slash (https://phenix-online.org/download) gets to a
different page with the right information! Must be something relatively obscure
about how URLs are interpreted. I’m using Safari in case other people are
having a different experience...
Best wishes,
Randy Read
> On 17 Jan 2024, at 19:12, Paul Adams wrote:
>
> 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:
>
> h...@phenix-online.org and b...@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.
>
> --
> 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: -0001-9333-8219
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 91R0183
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ]
> Phenix