The Phenix developers are pleased to announce that version 1.20 of Phenix is
now available (build 1.20-4459). Binary installers for Linux, Mac OSX, and
Windows platforms, and the source installer, are available at the download site:
http://phenix-online.org/download/
Highlights for the 1.20 version of Phenix include a number of tools to leverage
new structure prediction methods:
- New tools and methods
- Phenix AlphaFold2 notebook: Run AlphaFold on Google Colab from Phenix GUI
- phenix.process_predicted_model: Identify useful domains in AlphaFold model
- phenix.dock_predicted_model: Dock domains of AlphaFold model into cryo-EM
- phenix.rebuild_predicted_model: Rebuild AlphaFold model in cryo-EM map
using docked domains
- phenix.dock_and_rebuild : Process, dock and rebuild AlphaFold model with
cryo-EM map
- phenix.model_completion: Connect fragments and fill in gaps based on a map
- phenix.rebuild_model: Rebuild a model using a map and keeping connectivity
- phenix.replace_with_fragments_from_pdb: Rebuild a model using fragments
from PDB
- phenix.search_and_morph: SSM search PDB; morph to match target
- phenix.fragment_search: Search for a fragment in PDB matching target
- phenix.reverse_fragment: Reverse chain direction of a fragment
- phenix.superpose_and_morph: SSM or least-squares superpose one model on
another;
optionally trim and morph to match
- phenix.voyager.casp_rel_ellg: Calculate relative eLLG score for predicted
model quality
- phenix.match_maps:
- Bug fix (superposed map was not matching target map)
- phenix.real_space_refine:
- Symmatry multiprocessing aware individual ADP and occupancy refinement
- Multiple changes to improce runtime (for certain refinement strategies)
- Make NQH flips symmetry aware
- phenix.superpose_pdbs:
- Add feature to transform additional models with matrix found with moving
model
- phenix.dock_in_map:
- Allow splitting model into domains based on chain ID from
phenix.process_predicted_model
- Restraints
- GeoStd updated with 12k plus entity restraints files
- cis-PRO default updated to EH99
- phenix.fetch_pdb, iotbx.cif_as_mtz:
- Bug fix: Multiple datasets with different unit cells in a cif file now
preserved
as multiple crystals in mtz file.
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 principally 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/leadership/)
Principal Investigator, Computational Crystallography Initiative, LBL
(https://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute
(http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source
(https://als-enable.lbl.gov)
Division Deputy for Biosciences, Advanced Light Source (https://als.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 33, Room 250
Building 978, Room 4126
Building 977, Room 268
Tel: 1-510-486-4225
http://cci.lbl.gov/paul
ORCID: 0000-0001-9333-8219
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
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 ]
--
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