Pedro I used the documentation index to find
https://phenix-online.org/documentation/reference/AQuaRef.html so you can move ahead while we fix the route you used. Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Tue, Jan 13, 2026 at 12:57 AM Pedro Matias < [email protected]> wrote: > Dear Paul and colleagues, > > Thanks for the announcement. From your description of the changes it seems > to be a really exciting release with many innovations. > > I am currently downloading the Linux command line installer and I notice > there is another installer that begins with "CUDA 12". Does this mean that > you need CUDA v12 to be able to run it? > > Also, I am very curious about the aquaref option, however there is only a > line in the documentation page without an active link: > > AQuaRef: AI-enabled Quantum Refinement of macromolecular models > <AQuaRef.html> > > Is this a bug? > > Thanks & best regards, > > Pedro Matias > > > Às 23:00 de 12/01/2026, Paul Adams escreveu: > > 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: 1-510-486-4225http://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 ] > -- > > ######################################################################## > > 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/ > > -- > Industry and Medicine Applied Crystallography > Macromolecular Crystallography Unit > ___________________________________ > Phones : (351-21) 446-9100 Ext. 1669 > (351-21) 446-9669 (direct) > Fax : (351-21) 441-1277 or 443-3644 > > email : [email protected] > http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallographyhttp://www.itqb.unl.pt/labs/macromolecular-crystallography-unit > > Mailing address : > Instituto de Tecnologia Quimica e Biologica António Xavier > Universidade Nova de Lisboa > Av. da República > 2780-157 Oeiras > PORTUGAL > > ITQB NOVA, a great choice for your PhDhttps://youtu.be/de6j-aaTWNQ > > Master Programme in Biochemistry for Healthhttps://youtu.be/UKstDCFjYI8 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
