Supported Applications

PHENIX

Description

(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-cli install phenix
Primary Citation*

D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B. Hintze, L. W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams, and P. D. Adams. 2019. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta crystallographica. Section D, Structural biology. 75: 861-877.
- *Full citation information available through
Citation Note

Citations for all software packages used in a given project can also be generated from within PHENIX.
Tales

Structures Solved Simply

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 …
Read More.
Webinars

Topic: Atomic model, map and model-to-map fit validation
Part I: Atomic model validation
Speaker: Pavel Afonine, Berkeley Lab

Host: Jason Key
Recorded on April 14, 2020

Topic: Map Sharpening; Model Building; other cryo-EM tools in Phenix
Presenter: Dorothee Liebschner, Berkeley Lab

Hosted by Jason Key
Recorded on April 7, 2020

Topic: Atomic model refinement and validation in Phenix
Presenter: Pavel Afonine, Computational Research Scientist, Berkeley Lab

Date recorded: April 3, 2020

Host: Pete Meyer

Topic: Density Modification and Model Building with cryo-EM maps.
Presenter: Tom Terwilliger, Laboratory Fellow, Los Alamos National Laboratory

Recorded on March 31, 2020
Host: Jason Key

Link to slides: https://drive.google.com/open?id=1SHQ...

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

Host: Jason Key
Recorded on May 16, 2013