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Phenix

PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Download the latest official release ( 1.13. First request download password. Download the latest nightly build or prerelease. Subscribe to Mailing List. Using PHENIX (release 1.13):. The PHENIX Graphical User Interface. Assessing data quality with phenix.xtriage. Automated structure solution with AutoSol. Automated molecular replacement with Phaser-MR. For more details. C...

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Lawrence Berkeley National Laboratory

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Phenix | phenix-online.org Reviews

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PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Download the latest official release ( 1.13. First request download password. Download the latest nightly build or prerelease. Subscribe to Mailing List. Using PHENIX (release 1.13):. The PHENIX Graphical User Interface. Assessing data quality with phenix.xtriage. Automated structure solution with AutoSol. Automated molecular replacement with Phaser-MR. For more details. C...

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Phenix | phenix-online.org Reviews

https://phenix-online.org

PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Download the latest official release ( 1.13. First request download password. Download the latest nightly build or prerelease. Subscribe to Mailing List. Using PHENIX (release 1.13):. The PHENIX Graphical User Interface. Assessing data quality with phenix.xtriage. Automated structure solution with AutoSol. Automated molecular replacement with Phaser-MR. For more details. C...

INTERNAL PAGES

phenix-online.org

1

The phenix graphical interface

http://www.phenix-online.org/documentation/phenix_gui.html

The phenix graphical interface. Running programs from the GUI. The main GUI is started simply by typing the command. By default, it will also open automatically when you launch any of the individual program GUIs. You should not run more than one instance of the GUI at a time, to avoid conflicts with internal database files. Running programs from the GUI. Calculate R-sym, R-meas, mean I/sigma, CC1/2, and related statistics starting from scaled, unmerged intensities. With all parameters available as well a...

2

Model building (and more) in the AutoBuild GUI

http://www.phenix-online.org/documentation/reference/autobuild_gui.html

Model building (and more) in the AutoBuild GUI. Multiprocessing and queueing systems. NOTE: this document is mainly an introduction for users who are not familiar with AutoBuild (or the GUI), rather than a comprehensive reference for the program. The documentation for the command-line version. Covers the full range of options and functionality. Phenix.find helices strands. Phenix.phase and build. Several other programs have features similar to functions in AutoBuild; in particular, phenix.refine. AutoBui...

3

Phenix Download

http://www.phenix-online.org/download

Academic users can obtain a password for downloading Phenix. Via email. For industrial users, a separate password is required ( more information. Latest official release: 1.10.1-2155 (10-06-2015). Phenix development release with contributions from University of Cambridge, Duke University, LANL, LBNL; includes the Phenix GUI. Nightly builds and Prereleases. The PHENIX graphical interface includes extensions for Coot and PyMOL. Information on obtaining these is here.

4

PHENIX Documentation

http://www.phenix-online.org/documentation

Phenix Documentation - version 1.10-2155. Phenix programs and their functions. The Phenix graphical interface. Dictionary of crystallographic and other terms. FAQs: Frequently asked questions. How to install, setup and run Phenix. Complete Phenix reference documentation. Crystallographic Structure Solution with Phenix. Phenix Documentation for X-ray Crystallography. Phenix Documentation for Neutron Crystallography. Phenix Documentation for Electron Microscopy (EM). Convert map to structure factors.

5

cctbxbb Info Page

http://www.phenix-online.org/mailman/listinfo/cctbxbb

Cctbxbb - cctbx mailing list. To see the collection of prior postings to the list, visit the cctbxbb Archives. To post a message to all the list members, send email to cctbxbb@phenix-online.org. You can subscribe to the list, or change your existing subscription, in the sections below. You may enter a privacy password below. This provides only mild security, but should prevent others from messing with your subscription. Do not use a valuable password. Reenter password to confirm:. If you leave the field ...

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bioxtal.spring8.or.jp

構造生物学ビームライン

http://bioxtal.spring8.or.jp/ja/links/links_ja.html

SPring-8 Public User Information. The D-Cha interface is customized for Firefox version 2 or above. From outside of SPring-8, use https and a digital certificate is required. RIKEN Structural Genomics and Structural Biology Beamlines. Structural Biology Research Center. Intensity Integration of Diffraction Images. Shake and Bake (SnB). X-ray Form Factor, Attenuation, and Scattering Tables, NIST. The Dundee PRODRG2 Server.

strynadkalab.biochem.ubc.ca

Resources | Natalie Strynadka Lab | University of British Columbia

http://www.strynadkalab.biochem.ubc.ca/resources

UBC Biochemistry and Molecular Biology. Membrane proteins of known structure. Structure validation and analysis. Kevin Cowtan’s Book of Fourier. The Interactive Structure Factor Tutorial. Biochemistry and Molecular Biology. P2 complete genome sequencing project). Composite Protein Sequence Database). Biological Sequence Analysis group - Cambridge). Expert Protein Analysis System). Multiple Sequence Alignment for Proteins. Plot Amino Acid Physico-chemical Properties). Other Mol. Biol. Companies. SFU polic...

hartlab.uthscsa.edu

The University of Texas Health Science Center - X-ray Crystallography Core Laboratory

http://hartlab.uthscsa.edu/publications.php

Crystallization Screens Available to the Lab. Expression of a selenomethionine variant in E. coli. General molecular biology methods. Biological Macromolecule Crystallization Database. DynDom - Protein Domain Movement. PARVATI - Protein Anisotropic Refinement Validation and Analysis Tool. PDB Structure Validation Server. SAVS - Structure Analysis and Verification Server. STAN - Structure Analysis Server. Uppsala Software Factory - Crystallography Tools. WHATCHECK - Structure validation. J Biol. Chem.

cci.lbl.gov

Homepage for Paul Adams

http://cci.lbl.gov/paul

Paul D. Adams. Division Director, Molecular Biophysics and Integrated Bioimaging. Senior Scientist, LBNL and Adjunct Professor, Dept. Bioengineering. Division Deputy for Biosciences, Advanced Light Source. Vice President for Technology, the Joint BioEnergy Institute. Laboratory Research Manager, ENIGMA. Office: Building 33, Room 347, Lawrence Berkeley Laboratory. Paul Adams @ Google Scholar. Paul Adams @ PubMed. Much of my research is focused on the development of new algorithms and methods. The need to ...

sibyls.als.lbl.gov

The SIBYLS Beamline: Macromolecular Crystallography Programs

http://sibyls.als.lbl.gov/xtalprogs/xtalprogs.php

Brought to you by IDAT. We must become the change we want to see." -.

balavenkats.com

Inside The Blue: Tools I like

http://www.balavenkats.com/p/tools-i-like.html

There is a light that never goes out. Tons of web-based biological sequence-based tools. Good tools for PDB mining and analysis. Virus capsid specific Cryo-EM and PDB database with synchronized coordinates and orientations. Also some tools for building and analysis. Old-fashioned suite for crystallography and NMR structure determination and analysis. Powerful suite of programs for crystal structure determination. The present and future of macromolecular crystallography directed towards automation. Listen...

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Phenix

PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Download the latest official release ( 1.13. First request download password. Download the latest nightly build or prerelease. Subscribe to Mailing List. Using PHENIX (release 1.13):. The PHENIX Graphical User Interface. Assessing data quality with phenix.xtriage. Automated structure solution with AutoSol. Automated molecular replacement with Phaser-MR. For more details. C...

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