Dear Colleagues,
The Phenix developers are excited to announce that version 2.2 of Phenix is now
available (build 2.2-6143). Binary installers for Linux, Mac OSX, and Windows,
and the source installer, are available at the download site:
http://phenix-online.org/download
Highlights for this new version of Phenix include:
- phenix.agent: (NEW!) run Phenix and Coot tools via an agent using natural
language
- Added MCP server and skills for running Phenix with an agent
- phenix.validate_ligands: (NEW!) per-ligand validation of real-space fit (RSCC
for the ligand and its surroundings), difference density, clashes and H-bonds,
ADPs and occupancies (ligand vs. environment), geometry outliers, missing atoms
and alternative conformations, available in the GUI, with a results table,
per-ligand details and CSV export and replaces
mmtbx.development.validate_ligands
- phenix.pdb_deposition: (NEW!) start PDB deposition and upload model and data
files from Phenix
- phenix.find_reference: now with GUI
- Phenix now uses the new fast xcif parser
- Updated Nucleic Acid restraints (ideal and e.s.d.)
- Coot 1.3.1 included in Mac and Linux installers
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 previously 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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