CINXE.COM
Phenix
<!DOCTYPE html> <html lang="en" class="h-100"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1"> <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags --> <meta name="description" content="Phenix online main site"> <meta name="author" content="Phenix group"> <title>Phenix</title> <!-- Bootstrap CSS --> <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.1/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-+0n0xVW2eSR5OomGNYDnhzAbDsOXxcvSN1TPprVMTNDbiYZCxYbOOl7+AMvyTG2x" crossorigin="anonymous"> <!-- jQuery library --> <script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"> </script> <!-- JavaScript Bundle with Popper --> <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.1/dist/js/bootstrap.bundle.min.js" integrity="sha384-gtEjrD/SeCtmISkJkNUaaKMoLD0//ElJ19smozuHV6z3Iehds+3Ulb9Bn9Plx0x4" crossorigin="anonymous"></script> <!-- icons --> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.5.0/font/bootstrap-icons.css"> <!-- Custom CSS --> <link rel="stylesheet" href="/phenixwebsite_static/mainsite/css/mainsite.css" type="text/css"> <!-- --> <!-- Favicons --> <!-- <link rel="apple-touch-icon" href="/docs/5.0/assets/img/favicons/apple-touch-icon.png" sizes="180x180"> <link rel="icon" href="/docs/5.0/assets/img/favicons/favicon-32x32.png" sizes="32x32" type="image/png"> <link rel="icon" href="/docs/5.0/assets/img/favicons/favicon-16x16.png" sizes="16x16" type="image/png"> <link rel="manifest" href="/docs/5.0/assets/img/favicons/manifest.json"> <link rel="mask-icon" href="/docs/5.0/assets/img/favicons/safari-pinned-tab.svg" color="#7952b3"> <link rel="icon" href="/docs/5.0/assets/img/favicons/favicon.ico"> <meta name="theme-color" content="#7952b3"> --> </head> <body class="d-flex flex-column h-100"> <header> <div class="collapse" id="navbarHeader"> <div class="container"> <div class="row"> <div class="col-sm-6 col-md-6 py-4"> <h4>About</h4> <p>Phenix is a comprehensive software package for macromolecular structure determination that handles data from diffraction (X-ray, neutron and electron) and electron cryo-microscopy. Tasks include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Developers emphasize automation to minimize repetitive and time-consuming manual tasks. The graphical user interface streamlines the transition between programs, project tracking and re-running of previous tasks.</p> </div> <div class="col-sm-6 col-md-6 py-4"> <div class="row"> <div class="col"> <h4>Links</h4> <ul class="list-unstyled"> <li><a href="/download">Download Phenix</a></li> <li><a href="/getting_started">Getting Started</a></li> <li><a href="/workshops_tutorials">Workshops & Tutorials</a></li> <li><a href="/documentation/">Documentation</a></li> <li><a href="/help">Get Help</a></li> <li><a href="/people">Phenix Developers</a></li> <li><a href="/national_resource">Phenix National Resource</a></li> <li><a href="/consortium">Phenix Industrial Consortium</a></li> <li><a href="/metrics">Metrics</a></li> <li><a href="/newsletter">Newsletter</a></li> <li><a href="/papers">Publications</a></li> <li><a href="http://cci.lbl.gov/docs/cctbx/">cctbx</a></li> </ul> </div> <div class="col"> <h4>More</h4> <ul class="list-unstyled"> <li><a href="/about">About Phenix</a></li> <li><a href="/documentation/CHANGES">What's New</a></li> <li><a href="/presentations">Presentations</a></li> <li><a href="https://cci.lbl.gov/ceres">CERES Server</a></li> <li><a href="https://prediction.phenix-online.org/">Phenix Prediction Server</a></li> <li><a href="/phenix_data">Download Data</a></li> <li><a href="https://cci.lbl.gov/docs/phenix/">Phenix Developers Documentation</a></li> <li><a href="/license">Licensing</a></li> <li><a href="/acknowledge">Acknowledgements</a></li> <li><a href="/contact">Contact Us</a></li> </ul> </div> </div> </div> </div> </div> </div> <div class="navbar navbar-light shadow-sm"> <div class="container"> <a href="/" class="navbar-brand d-flex align-items-center"> <img src="/phenixwebsite_static/mainsite/img/phenix-logo-1.jpg" height="200"> <!-- <strong>Software package for macromolecular structure determination</strong> --> </a> <!-- <form action="http://www.google.com/search" method="get"role="search"> <div class="row g-3 align-items-center mt-3"> <div class="col-auto"> <label for="PhenixOrgSearch" class="col-form-label">Search Phenix website</label> </div> <div class="col-auto"> <input type="text" name="q" size="30" class="form-control" maxlength="255" value=""> <input type="hidden" name="sitesearch" value="http://cci2.lbl.gov:8080/phenixwebsite/mainsite/"> </div> </div> </form> --> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarHeader" aria-controls="navbarHeader" aria-expanded="false" aria-label="Toggle navigation"> <span style="margin-right: 10px;">Menu</span> <span class="navbar-toggler-icon"></span> </button> </div> </div> </header> <main class="flex-shrink-0"> <!-- ----------------------------------------------------------------------- --> <div class="bg-light"> <section class="py-4 text-center container "> <div class="row row-cols-1 row-cols-sm-1 row-cols-md-1 "> <div class="col-lg-2"></div> <div class="col-lg-8"> <span class="lead" style="font-size: 26px;"><b>A comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and electron cryo-microscopy data.</b> <a href="/about"><i class="bi bi-link"></i> Learn more</a></span> </div> <div class="col-lg-2"></div> </div> </section> </div> <!-- ----------------------------------------------------------------------- --> <section class="py-5 text-center container"> <div id="carouselIndex" class="carousel carousel-dark slide carousel-fade" data-bs-ride="carousel"> <div class="carousel-indicators"> <button type="button" data-bs-target="#carouselIndex" data-bs-slide-to="0" class="active" aria-current="true" aria-label="Slide 1"></button> <button type="button" data-bs-target="#carouselIndex" data-bs-slide-to="1" aria-label="Slide 2"></button> <button type="button" data-bs-target="#carouselIndex" data-bs-slide-to="2" aria-label="Slide 3"></button> <button type="button" data-bs-target="#carouselIndex" data-bs-slide-to="3" aria-label="Slide 4"></button> </div> <div class="carousel-inner"> <!-- ****************************************************************************** Content of slide show ****************************************************************************** --> <!-- The figures in the slide show should have size 1000 x 750 with 72 dpi. This way, they are all the same size. Resizing with style does not look as coherent. --> <div class="carousel-item active" data-bs-interval="6000"> <div class="row text-start carouselRow" > <div class="col-lg-4 d-none d-lg-block"> <center><a href="/about"><i class="img-fluid bi bi-info-circle" style="font-size: 12rem; color: cornflowerblue;"></i></a></center> <!-- <center><i class="img-fluid bi bi-info-circle" style="font-size: 12rem; color: cornflowerblue;"></i></center> --> <!-- <img class="img-fluid" src="/phenixwebsite_static/mainsite/img/index_alphafold.png"> --> </div> <div class="col-lg-8"> <span style="font-size: 32px;">New Phenix Release (version 1.21)</span> <ul class="mt-3" style="font-size: 20px;"> <li>Highlights</li> <ul> <li>Likelihood-based docking of models into cryo-EM maps (<a href="https://journals.iucr.org/d/issues/2023/04/00/vo5011/index.html">article</a>).</li> <li>Full support for structure determination with AlphaFold models (<a href="https://www.nature.com/articles/s41592-023-02087-4">article</a>).</li> <li>New joint X-ray and neutron refinement (<a href="https://pubmed.ncbi.nlm.nih.gov/37942718/">article</a>).</li> </ul> <li>Full list of changes: <a href="https://phenix-online.org/version_docs/1.21-5207/CHANGES">Changelog</a></li> <div class="mt-2"><a href="/download">Download</a></div> </ul> </div> </div> </div> <div class="carousel-item" data-bs-interval="6000"> <div class="row text-start carouselRow" > <div class="col-lg-4 d-none d-lg-block"> <img class="img-fluid" src="/phenixwebsite_static/mainsite/img/index_alphafold.png"> </div> <div class="col-lg-8"> <span style="font-size: 32px;">Phenix integrated with AlphaFold</span> <ul class="mt-3" style="font-size: 20px;"> <li>Structure determination with AlphaFold <a href="https://youtu.be/q3PemBu8RB0">video tutorial</a></li> <li>Predict a structure on the Phenix AlphaFold server <a href="https://youtu.be/D6y-wXnwZYM">video tutorial</a></li> <li>PredictAndBuild (Xray) <a href="https://youtu.be/4LL7pQ60lc8">video tutorial</a></li> <li>PredictAndBuild (cryo-EM) <a href="https://youtu.be/lrpB_GtpIkU">video tutorial</a></li> <div class="mt-2"><a href="documentation/reference/alphafold.html">Learn more</a></div> </ul> </div> </div> </div> <div class="carousel-item" data-bs-interval="6000"> <div class="row text-start carouselRow" > <div class="col-lg-4 d-none d-lg-block"> <img class="img-fluid" src="/phenixwebsite_static/mainsite/img/index_gui.png"> </div> <div class="col-lg-8"> <span style="font-size: 32px;">What Phenix can do for you:</span> <ul class="mt-2" style="font-size: 20px;"> <li>Experimental Phasing (crystallography)</li> <li>Molecular Replacement</li> <li>Automated model building (cryo-EM and crystallography)</li> <li>Refinement (real space and reciprocal space)</li> <li>Validation</li> <div class="mt-2"><a href="/about">Learn more</a></div> </ul> <!-- <a href="/about">Learn more</a> --> </div> </div> </div> <div class="carousel-item" data-bs-interval="6000"> <div class="row text-start carouselRow" > <div class="col-lg-4 d-none d-lg-block"> <img class="img-fluid" src="/phenixwebsite_static/mainsite/img/workshop.jpeg"> </div> <div class="col-lg-8"> <span style="font-size: 32px;">Workshops:</span> <div class="mt-3" style="font-size: 20px;"> <b>Next workshop:</b><br> <!-- TBD --> No user workshop is currently scheduled. <!-- Phenix user workshop at Berkeley Lab, 3/7/2024: <a href="/workshop_agenda">Agenda</a>.<br> --> <!-- Phenix user workshop at the University of Kansas: <a href="https://psxl.ku.edu/structural-biology-workshop">https://psxl.ku.edu/structural-biology-workshop</a>.<br> --> <br> See the recordings of past workshops: <br> <a href="https://www.youtube.com/playlist?list=PLAZ_ylz4cCoN9rr1UOXX10LGXw1RJvKee">YouTube Playlist</a><br> <a href="/workshops_tutorials">Workshops overview</a> </div> </div> </div> </div> </div> <!-- end carousel inner --> <button class="carousel-control-next" type="button" data-bs-target=" #carouselIndex" data-bs-slide="next"> <span class="carousel-control-next-icon" aria-hidden="true"></span> <span class="visually-hidden">Next</span> </button> </div> <!-- end carouselExampleDark --> </section> <!-- ----------------------------------------------------------------------- --> <div class="album py-5 bg-light"> <div class="container"> <div class="row row-cols-1 row-cols-sm-2 row-cols-md-3 row-cols-lg-4 g-5"> <div class="col"> <a href="/download" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-cloud-arrow-down"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Download</center></h4> </div> </a> </div> <div class="col"> <a href="/getting_started" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-hand-index" ></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Getting Started</center></h4> </div> </a> </div> <div class="col"> <a href="/workshops_tutorials" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-easel"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Workshops & Tutorials</center></h4> </div> </a> </div> <div class="col"> <a href="documentation/" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-book"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Documentation</center></h4> </div> </a> </div> <div class="col"> <a href="/help" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-question-circle"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Help</center></h4> </div> </a> </div> <div class="col"> <a href="/people" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-person-circle"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Developers</center></h4> </div> </a> </div> <div class="col"> <a href="/national_resource" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-globe"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>National Resource</center></h4> </div> </a> </div> <div class="col"> <a href="/consortium" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-bounding-box"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Industrial Consortium</center></h4> </div> </a> </div> <div class="col"> <a href="/metrics" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-bar-chart"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Metrics</center></h4> </div> </a> </div> <div class="col"> <a href="/newsletter" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-newspaper"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Newsletter</center></h4> </div> </a> </div> <div class="col"> <!-- <a href="/papers" class="card border-0 MyCard"> --> <a href="https://scholar.google.com/citations?view_op=list_works&hl=en&authuser=4&hl=en&user=gEiM6kIAAAAJ&authuser=4" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-file-text"></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>Publications</center></h4> </div> </a> </div> <div class="col"> <a href="http://cci.lbl.gov/docs/cctbx/" class="card border-0 MyCard"> <div class=" CardBlue"> <center><i class="bi bi-wrench"></i></i></center> </div> <div class="card-body"> <h4 class="card-title"><center>cctbx</center></h4> </div> </a> </div> </div> </div> </div> <!-- ----------------------------------------------------------------------- --> <div class="py-5"> <div class="container"> <p> <b>Citing Phenix:</b><br> <strong>Macromolecular structure determination using x-rays, neutrons and electrons: recent developments in phenix.</strong> D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunk贸czi, V. B. Chen, T. I. Croll, B. Hintze, L. W. Hung, S. Jain, A. J. <span class="bibtex-protected">McCoy</span>, 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, P. D. Adams. <em>Acta Crystallogr D Struct Biol</em> <strong>75</strong>, 861–877 (2019). <a href="https://doi.org/10.1107/S2059798319011471">doi:10.1107/S2059798319011471</a>. </p> <p> <b>Phenix Development, Maintenance and Distribution is Supported by:</b><br> NIH/NIGMS Program Project Grant (P01GM063210)<br> NIH/NIGMS R24 National Resource Grant (R24GM141254)<br> The Phenix Industrial Consortium </p> </div> </div> <!-- ----------------------------------------------------------------------- --> </main> <footer class="footer mt-auto text-muted py-3 bg-light"> <div class="container "> <div class="row row-cols-2 row-cols-md-4"> <!-- <div class="col-sm-3 offset-md-1 py-4"> --> <div class="col py-3"> <h4>Contact</h4> <ul class="list-unstyled"> <!-- <li><a href="#" >Follow on Twitter</a></li> --> <li><a href="/cdn-cgi/l/email-protection#1c7479706c5c6c74797275643173727075727932736e7b">Email us</a></li> </ul> </div> <div class="col py-3"> <h4>Disclaimer</h4> <a href="https://www.lbl.gov/Disclaimers.html">Privacy & Security Notice</a><br> <a href="/about_this_website">About this website</a> </div> <div class="col py-3"> </div> <div class="col py-3"> <p class="float-end mb-1"> <a href="#">Back to top</a> </p> </div> </div> </div> </footer> <script data-cfasync="false" src="/cdn-cgi/scripts/5c5dd728/cloudflare-static/email-decode.min.js"></script></body> </html>