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 athttps://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] [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 ]
--
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Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___________________________________
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(351-21) 446-9669 (direct)
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email :[email protected]
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PORTUGAL
ITQB NOVA, a great choice for your PhD
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