(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
Usage Notes
If you use PHENIX to solve a structure please cite this publication:
PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002)
Installation
Use the following command to install this title with the CLI client: $ sbgrid install phenix
Primary Citation*
P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, and P. H. Zwart. 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta crystallographica Section D: Biological crystallography. 66(2): 213-221.
*Full citation information available through
Citation Note
Citations for all software packages used in a given project can also be generated from within PHENIX.
It used to be that to book a trip you'd first need to call every airline to compare flights. Then you'd need to find good hotel deals. Then you'd have to revisit the flights. And so on. The same trial and error approach also used to hold true for structural biology. Frequent failures made scientists all too familiar with square one.
Now, however, what Orbitz and Expedia have done for travel, Phenix has done for structural biology.
Phenix helps investigators solve Xray crystal structures using multiple approaches, including molecular replacement and experimental phasing. It makes things easier by streamlining these multi-step procedures programmatically. Experimental data goes in, and a solution comes out.
Phenix Wizards perform the magic. For instance, the autosol program drives experimental phasing by pre-processing experimental …
Topic: Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix Presenter: Nigel Moriarty, Lawrence Berkeley National Labs
Host: Pete Meyer Recorded on: October 8, 2019
Topic: Getting the most out of your XFEL data with IOTA and PRIME Presenters: Mona Uervirojnangkoorn, Postdoctoral Associate and Art Lyubimov, HHMI Research Specialist Axel Brunger's Group, Stanford University
Host: Jason Key Recorded on January 17, 2017
Topic: Processing serial crystallographic data using cctbx.xfel and DIALS Presenter: Aaron Brewster, Project Scientist, Lawrence Berkeley National Laboratory
Host: Jason Key Recorded on January 10, 2016
Topic: Cctbx.xfel: New software for serial crystallography Presenter: Nicholas Sauter, Lawrence Berkeley National Laboratory
Presented as part of: SBGrid/NE-CAT 2014: Data Processing in Crystallography June 5-6, 2014
Topic: Refinement of challenging structures with Rosetta and Phenix Presenter: Nat Echols, Computational Scientist at Lawrence Berkeley National Labs
Host: Andrew Morin Recorded on May 13th, 2014
Topic: Extending the reach of molecular replacement in Phaser Presenter: Randy Read, Wellcome Trust Principal Research Fellow in the Department of Haematology at University of Cambridge.
Host: Piotr Sliz Recorded on April 23, 2012
Topic: Phenix: Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution Presenter: Jeff Headd, Postdoctoral Fellow at Lawrence Berkeley National Laboratories
Host: Piotr Sliz Recorded on December 12, 2011
Topic: ERRASER for RNA structure error correction Presenter: Steven Lewis, postdoc,Richardson Laboratory, Duke University Presenter: Jane Richardson, Professor, Duke University
