Dear Colleagues, The Phenix developers are pleased to announce that the long awaited version 2.0 of Phenix is now available (build 2.0-5936). Binary installers for Linux, Mac OSX, and Windows, and the source installer, are available at the download site: http://phenix-online.org/download This is the first official release of Phenix that is based on Python 3. Moving forward, Python 2 will no longer be supported. Other highlights for this new version of Phenix include: - Phenix help chatbot available at https://phenix-online.org/chatbot - AI analysis of result files available in GUI (non-commercial only, requires free Google and Cohere API keys) - phenix.aquaref: Full-model AI-accelerated quantum refinement for crystallography & cryo-EM - phenix.refine: - occupancy refinement for water is now the default - use longer X-H distances if scattering table is 'electron' (for electron diffraction, cryoEM) - rotamer fitting for aa side chains with alternative conformations (use fit_altlocs_method, not the default) - alternative conformation aware water picking (use include_altlocs, not the default) - phenix.real_space_refine: option to refine two group ADP per residue (main and side chain) - phenix.fit_h: optimize position of H atoms with rotational degrees of freedom against density map - phenix.magref: new tool for pixel size (magnification) refinement for cryoEM - phenix.renumber_fab: (NEW!) renumber FAB chains using Kabat, Chothia or Martin conventions - phenix.find_reference: (NEW!) automatically find and prepare reference model - phenix.holton_geometry_validation: Composite geometry validation score - phenix.create_alt_conf: Create model with alternative conformations using high-resolution data - phenix.process_predicted_model: Allow alternative defaults to work better using pae matrix - phenix.combine_focused_maps: allow applying both normalization and scale factors - phenix.ligandfit: Trim model outside of map area for cryo-EM maps - phenix.fetch_pdb: added ability to download Cryo-EM data - phenix.map_correlations (calculates map-map and map-model correlations, with optional translational offsets) replaces phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, phenix.map_model_cc, phenix.model_map_cc, and phenix.get_cc_map_map 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: [email protected] and [email protected] Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix has been funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is currently 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) 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 [ [email protected] ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ [email protected] ][ 1-510-486-5455 ] --