CINXE.COM

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>ACA CryoEM Workshop 2018 : EMDataResource</title> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">  <script async src="https://www.googletagmanager.com/gtag/js?id=G-0N32KDVZDG"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-0N32KDVZDG'); </script> <meta property="og:title" content="EMDataResource" /> <meta property="og:type" content="website" /> <meta property="og:url" content="https://www.emdataresource.org" /> <meta property="og:image" content="/images/EMDataResource-logo-small.png" /> <link rel="shortcut icon" href="/favicon.ico"> <link href="/css/bootstrap4.1.3.min.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <link href="/css/em-styles-cutdown.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <link href="/css/navbar.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <script src="/js/jquery-3.3.1.min.js" type="text/javascript"></script> <script src="/js/popper1.12.9.min.js" type="text/javascript"></script> <script src="/js/bootstrap4.1.3.min.js" type="text/javascript"></script> <script type="text/javascript" src="/js/bootstrap3-typeahead.min.js"></script> </head> <body> <div class="container"> <div class="card" style="border: none; margin-bottom: 0px;" > <div class="card-header clearfix" style="background-color: #CCC;"> <div class="float-left"><b><span id="siteid"></span></b></div> <script> var sitebanner="" if (location.hostname.search("test") != -1) {sitebanner = "PRE-PRODUCTION STAGING SITE"; } if (location.hostname.search("159.51") != -1) {sitebanner = "PRE-PRODUCTION STAGING SITE"; } else if (location.hostname.search("dev") != -1) {sitebanner = "DEVELOPMENT SITE"; } else if (location.hostname.search("beta") != -1) {sitebanner = "BETA TESTING SITE"; } else if (location.hostname.search("4.80") != -1) {sitebanner = "REVIEW SITE"; } document.getElementById("siteid").innerHTML = sitebanner; </script> <div class="float-right"><span id="update_date">2025-02-19</span> : <span id="map_entries">42759</span> EMDB map entries, <span id="coordinate_entries">25065 PDB coordinate entries <a href="https://go.rutgers.edu/zcuqsog5" target="_blank">RCSB PDB</a> | <a href="https://go.rutgers.edu/paqlf60v" target="_blank" >PDBe</a> </span>  </div> </div> <div class="card-body" style="padding: 2px 15px;" > <div class="float-left"><a href="/index.html"> <img src="/images/EMDataResource-logo-small.png" alt="EMDataResource.org" height="78" style="margin-right: 25px;" /> </a></div> </div> <nav class="navbar navbar-expand-lg navbar-dark"> <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div class="collapse navbar-collapse" id="navbarSupportedContent"> <ul class="nav navbar-nav mr-auto"> <li class="nav-item"> <a class="nav-link" href="/index.html">Home</a></li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> About</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/mission.html">Mission</a> <a class="dropdown-item" href="/team.html">Team</a> <a class="dropdown-item" href="/dictionaries.html">Dictionaries</a> <a class="dropdown-item" href="/conventions.html">Conventions</a> <a class="dropdown-item" href="/validation.html">Validation</a> <a class="dropdown-item" href="/project_publications.html">Publications</a> <a class="dropdown-item" href="/funding.html">Funding</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/deposit.html">Deposit</a></li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Search</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/emdlist=all">EMDR Search</a> <a class="dropdown-item" href="/coronavirus_search.html">CoV Enhanced Search</a> <a class="dropdown-item" href="/solrfacet.html">EMDR Search Term Facet Tool</a> <a class="dropdown-item" href="/searchnonrel.html">Search Proc/Hold/Obs/Wdrn Entries</a> <a class="dropdown-item" href="/search.html">All EMDB Search Options</a> </div> </li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Tools</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/statistics.html">Statistics</a> <a class="dropdown-item" href="https://ptp.emdataresource.org">RNA Virtual Torsion Analysis</a> <a class="dropdown-item" href="/emsoftware.html">EM Software List</a> <a class="dropdown-item" href="/emtestdata.html">3DEM Test Data</a> <a class="dropdown-item" href="/emdbaccess.html">EMDB Access</a> </div> </li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Archive</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown">  <a class="dropdown-item" href="/challenges/index.html">EMDR Challenges</a> <a class="dropdown-item" href="/workshops.html">Workshops</a> <a class="dropdown-item" href="/emdbac.html">Advisory Committee</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/allnews.html">News</a></li> <li class="nav-item"><a class="nav-link" href="/externallinks.html">Links</a></li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Help</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/contactus.html">Contact Us</a> <a class="dropdown-item" href="/faq.html">FAQ</a> </div> </li> </ul> <form class="form-inline my-2 my-lg-0"> <input id="homequery" class="form-control typeahead mr-sm-2" data-sho-hint-on-focus="true" data-provide="typeahead" autocomplete="off" data-autoselect="false" type="search" placeholder="Search EMDB" aria-label="Search EMDB"> <button id="btnSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" style="background-color: #CCC;" ><img src="/images/search_icon.svg" alt="search" /></button> </form> </div> </nav> <div class="card-body"> <h2>2018 ACA CryoEM Workshop</h2> <p> The <a href="http://www.amercrystalassn.org/2018-workshops" target="_blank">Cryo-EM Workshop: A Guide to High Resolution Structure Determination</a> was held on July 21, 2018 as part of the American Crystallographic Association Annual Meeting in Toronto, Canada. Co-organized by Lori Passmore (MRC-LMB) and Wah Chiu (Stanford U), and sponsored by Douglas Instruments, Gatan, and ThermoFisher Scientific, the one-day workshop attracted over 130 attendees.</p> <br/>  <img src="../newsimages/ACAworkshop2018.png" alt="workshop image" width="100%" /> <br/> <br/> <p>Cryo-EM has become increasingly popular among structural biologists and is now the method of choice for structure determination of proteins larger than ~200 kDa. It has been particularly successful for proteins that are difficult to crystallize, including membrane proteins, large assemblies and multi-protein complexes. The workshop provided a detailed overview of cryo-EM specimen preparation, image processing and building/refinement of atomic models, with focus on high-resolution single particle cryo-EM, and several hands-on tutorials. Materials from the workshop can be accessed through the links below.</p> <br/> <p>Go to <a href="https://rutgers.box.com/s/cfbpq48fzz58b2l03yz9x4pqni0ql4li" target="_blank">this public Box folder</a> or <a href="https://www.dropbox.com/sh/daxe98rzm2ecyez/AAAyq6IYDwAB9Bl91ifEFVj1a?dl=0" target="_blank">this public DropBox folder</a> to access talk pdfs and workshop zip files.</p> <br/> <h2>Slides/Handouts</h2> <table class="table"> <tbody> <tr> <td><b>Instructor</b> </td> <td> <b>Topic </b></td></tr> <tr> <td>Wah Chiu </td> <td><a title="2018ACACryoEM_Chiu.pdf" target="_blank">Welcome and Introduction to Cryo-EM</a></td></tr> <tr> <td>Lori Passmore</td> <td><a title="2018ACACryoEM_Passmore.pdf" target="_blank">Specimen Preparation for Cryo-EM</a></td></tr> <tr> <td>Chris Russo</td> <td><a title="2018ACACryoEM_Russo.pdf" target="_blank">Specimen Preparation, Data Collection and Radiation Damage</a> || <a title="RussoHenderson2018c.pdf" target="_blank">Russo&Henderson2018</a></td></tr> <tr> <td>John Rubinstein</td> <td><a title="2018ACACryoEM_Rubinstein.pdf" target="_blank">Image Processing — Intro, Background, Implementation</a></td></tr> <tr> <td>Marcus Brubaker</td> <td><a title="2018ACACryoEM_Brubaker.pdf" target="_blank">Image Processing — Bayesian Methods and Optimization</a></td></tr> <tr> <td>Ali Punjani</td> <td><a title="2018ACACryoEM_Punjani.pdf" target="_blank">CryoSparc Image Processing Tutorial</a></td></tr> <tr> <td>Tom Terwilliger</td> <td><a title="2018ACACryoEM_Terwilliger.pdf" target="_blank">Phenix tools for Cryo-EM</a></td></tr> <tr> <td>Matthew Baker</td> <td><a title="2018ACACryoEM_Baker.pdf" target="_blank">Model Building in Cryo-EM</a> || <a title="2018ACACryoEM_Baker_pathwalking_tutorial.pdf" target="_blank">Pathwalking Tutorial</a></td></tr> <tr> <td>Corey Hryc</td> <td><a title="2018ACACryoEM_Hryc_optimization_tutorial.pdf" target="_blank">Model Optimization Tutorial</a> || <a title="2018ACACryoEM_T20S_optimization.zip" target="_blank">zipfile</a></td> </tr> <tr> <td>Corey Hryc</td> <td><a title="2018ACACryoEM_Hryc_validation_tutorial.pdf" target="_blank">Model Validation Tutorial</a> || <a title="2018ACACryoEM_T20S_validate.zip" target="_blank">zipfile</a></td> </tr> </tbody> </table> <br/> <h2>Tutorial Software</h2> These software packages are available on Mac, Linux and Windows. <ul> <li><a href="https://www.cgl.ucsf.edu/chimera/">UCSF Chimera</a> is used to visualize/manipulate both map and model. </li> <li><a href="https://www.phenix-online.org/">Phenix</a> (command line) is used to optimize the molecular model with respect to the experimental data.</li> <li><a href="http://blake.bcm.edu/emanwiki/EMAN2">EMAN2</a> is used for Pathwalking as well as validation routines such as map/model FSC. </li> <li><a href="https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/">COOT</a> is used for model refinement in the Pathwalker Tutorial.</li> </ul> <br/> <p>updated 24 July 2024</p> <br class="clearfloat" /> </div> <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="color:#666; background-color: #E4E4E4; padding-top: 18px; padding-bottom: 3px;"> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://cryoem.slac.stanford.edu" target="_blank"> <img src="/images/ncmi-logo.png" alt="Stanford-CryoEM" height="35px"/></a> </div> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://www.rcsb.org" target="_blank"> <img src="/images/rcsb-pdb-logo.png" alt="PDB" height="35px"/></a> </div> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://www.ebi.ac.uk/emdb/" target="_blank"> <img src="/images/EMDB_logo_2017.png" alt="EMDB" height="35px"/></a> </div> <div class="col-sm-6"> <div class="float-right text-right"> <p style="margin-bottom: 0px;"> Prior Support from<br />National Institutes of Health<br />National Institute of General Medical Sciences</p> </div> </div> </div> <div class="row" style="color:#FFF; background-color: #666; padding-top: 3px; padding-bottom: 8px;"> <div class="col-sm-2">   </div> <div class="col-sm-10"> <div class="small float-right text-right" style="margin-top: 8px;" > © 2007-2025 EMDataResource</div> </div> </div> </div> </footer> </div> </div>  <script> $.get("/js/auto.json", function(data){ $("#homequery").typeahead({ source: data, items: 8, minLength: 1, delay: 60, autoSelect: true, }); },'json'); $('#btnSearch').on('click', function () { var url; var searchInput = $('#homequery').val(); //minimum of 3 characters var regex0 = new RegExp ( "(.){3,}" ); var results0 = regex0.exec( searchInput ); if (results0 !== null) { //test for an EMDB id with or without "EMD-" prefix var regex1 = new RegExp ( "^[eE][mM][dD]-[0-9]{4,}$" ); var regex2 = new RegExp ( "^[0-9]{4,}$" ); //pure number 4+ digits var results1 = regex1.exec( searchInput ); var results2 = regex2.exec( searchInput ); if (results1 !== null) { url = "/EMD-" + searchInput.slice(4); window.open(url); } else if (results2 !== null) { url = "/EMD-" + searchInput; window.open(url); } else { url = "/?emdlist=" + searchInput; window.open(url); } } }); </script> </body> </html>