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 <pdad...@lbl.gov> 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: 0000-0001-9333-8219 > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 91R0183 > Berkeley, CA 94720, USA. > > Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ] > Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] > -- > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
