Dear Colleagues,
The Phenix developers are excited to announce that version 2.1 of Phenix is now available (build 2.1-6048). 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 AI agent available in GUI
- Add integration with Coot 1
- Fix integration with PyMOL
- Fix bug with reading 16-bit float MRC maps (mode 12)
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:
help(a)phenix-online.org and bugs(a)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 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.
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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 [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ]
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You are cordially invited to join the Center for Biomolecular Structure Lecture Series ………..
Guillermo Calero, MD PhD
University of Pittsburgh School of Medicine
WEDNESDAY, May 6, 13:30 (EDT)
"Fine-tuning Time Resolved Experiments to Capture Crystal Biochemistry"
Register in advance for this meeting:
https://bnl.zoomgov.com/meeting/register/TztZw5fpSr-kBHygBEuzwA
Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…>
Abstract: Typically, interactions between enzymes and substrates (or inhibitors), are viewed in terms of small molecules binding to relatively rigid proteins. However, computational and experimental studies demonstrate that proteins undergo a variety of molecular motions over a wide range of timescales. Such conformational flexibility is integral to enzyme activity, drug action and drug resistance. Contemporary structural biology approaches resolve only the structures of thermodynamically stable species. By contrast, time resolved (TR) structural studies using crystallography or single particle cryoEM are innovative tools that reveals details of both the ligand binding process and the stepwise chemistry of the reaction, with important biomedical applications. Through a combination of TR techniques, including UV photolysis of caged substrates, we have used TR techniques to create the first molecular movies of: 1) b-lactam antibiotics binding to b-lactamases; 2) deoxynucleotide addition by HIV-1 Reverse Transcriptase (RT); 3) nucleotide addition by RNA polymerase II (Pol II); and 4) GTP hydrolysis by N-RAS.
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Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e lifescience(a)bnl.gov<mailto:[email protected]>
w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/>
Address:
Center for Biomolecular Structure
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973
