pdb_extract

<!doctype html> <html>  <head> <meta charset="UTF-8" /> <title>pdb_extract</title> <meta name="description" content="pdb_extract is used to convert PDB format file to mmCIF format, and extract statistical information from the output files produced by many software for protein structure determination using Xray Crystallography and NMR methods" /> <meta name="keywords" content="pdb_extract, convert PDB to CIF, PDB conversion, mmCIF, CIF, PDB deposition, x-ray crystallography, data collection and reduction, molecular replacement, heavy atom phase determination, density modification, structure refinement, nmr structure determination, hkl/scalepack, d*trek, saint, scala(ccp4), xscale, mosflm, x-gen, cns/cnx/xplor, amore(ccp4), epmr, phaser,beast, solve, mlphare(ccp4), sharp/autosharp, shelxd/shelxs, phases, snb, bnp, bp3, dm(ccp4), solomon(ccp4), resolve, shelxe, refmac5(ccp4), restrain(ccp4), ccp4, shelxl, tnt, phenix, buster-tnt, arp/warp, cyana, xplor-nih" /> <link href="wwpdb_css/site.css" rel="stylesheet" type="text/css" media="all" />  </head> <body> <div class="container"> <header class="container_12"> <div class="logo"> <a href="https://www.wwpdb.org/"><img src="wwpdb_img/wwpdb_logo.gif" alt="pdb_extract Logo" width="187" height="58" /></a> </div> <div class="topnav frht bg-green ui-corner-all pall"> <a href="index.html" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-icon-only" title="Home"><span class="ui-button-text">Home</span></a> <a href="version.html" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-icon-only" title="Version"></span><span class="ui-button-text">Version</span></a> <a href="documentation.html" class="ui-button ui-widget ui-state-default ui-corner-all ui-button-icon-only" title="Documentation"><span class="ui-button-text">Documentation</span></a> <div class="clear"> </div> </div> <div class="headercontent prefix_1"> <h1>pdb_extract</h1> </div> <div class="clear"> </div> <div class="seperator"></div> </header> <div class="content container_12">  <p> pdb_extract is a pre-deposition service for assembling structure files for wwPDB OneDep<a href="https://deposit.wwpdb.org/"> deposition </a>.<br/> Use this online tool (<a href="tutorial.html">tutorials </a> available) or download the <a href="http://sw-tools.rcsb.org/apps/PDB_EXTRACT/source.html">standalone</a> program to run on your local machine. This tool will: </p> <ul> <li>Convert PDB format file to mmCIF format </li> <li>Prepare a re-usable template file of your metadata via PDBj's mmCIF Editor for <a href="/cgi-bin/pdbj_cif_editor_template_xray.pl">Xray</a>, <a href="/cgi-bin/pdbj_cif_editor_template_nmr.pl"> NMR</a>, <a href="/cgi-bin/pdbj_cif_editor_template_em.pl"> EM</a> (*Note: click Editor's upper-left gear icon to save/download or access help). The template can be uploaded at the next step, and used for multiple entries. </li> <li>Assemble coordinates and log files pertaining to your specific experimental methods. </li> <li>Allow you to update the primary sequence of your protein/nucleotide chains to account for unresolved residues. </li> </ul> <h3>How to Run:</h3> <ol> <li>Select the experimental method you used to solve the structure</li> <li>Select the type of structure model coordinates file to be uploaded</li> <li>Upload the finally refined structure model coordinate file</li> <li>Press the <strong>RUN</strong> button to start <strong>pdb_extract</strong> <li>The mmCIF files that you obtain can be used as input for wwPDB OneDep <a href="https://deposit.wwpdb.org/"> deposition </a>and <a target="_blank" href="http://wwpdb-validation.wwpdb.org/ ">validation</a>. </li> </ol> <h4>If you upload PDB format structure model coordinates file:</h4> <font color="red"> <li>1. The column alignment for <a href="https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM">ATOM</a> and/or <a href="https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM">HETATM</a> record rows must be correct.</li> <li>2. Please ensure that each polymer has a unique Chain ID in the file. If your uploaded file does not have chain ID, pdb_extract will try the best guess to add chain ID, and if so please review the chain ID addition on the next page.</li> <li>3. A <a href="https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#TER"> TER </a> card must be present at the end of each complete polymer chain, but a TER card should not be placed in the middle of a polymer chain even if there is a main-chain break due to disordered residues not built in the model.</li> </font> <form action="/cgi-bin/harv-main.cgi" method="post" enctype="multipart/form-data"> <fieldset class="brdr_dash ui-corner-all"> <div class="grid_3"> <label for="method_0">Select Experimental Method</label> </div> <div class="grid_9"> <input type="radio" name="method" value="XRAY" id="method_0" checked="" /> <label for="method_0">X-Ray</label> <input type="radio" name="method" value="NMR" id="method_1" /> <label for="method_1">NMR</label> <input type="radio" name="method" value="EM" id="method_2" /> <label for="method_2">EM</label> </div> <div class="clear"> </div> <br /> <div class="grid_3"> <label for="filetype_model_author">Select Type of Upload File</label> </div> <div class="grid_9"> <select name="filetype_model_author" id="filetype_model_author"> <option value=""></option> <option value="pdb">PDB </option> <option value="cif">mmCIF </option> </select> </div> <div class="clear"> </div> <br /> <div class="grid_3"> <label for="filename_model_author">Upload Structure Model Coordinate File</label> </div> <div class="grid_9"> <input type="file" name="filename_model_author" id="filename_model_author" /> </div> <div class="clear"> </div> <br />  <div class="clear"> </div> <br /> <div class="prefix_2"><center> <input type="submit" value="Run" name="submit"/> <input type="reset" value="Reset" /></center> </div> </fieldset> </form> <b>Note: </b> If the file size is too large (e.g. >100 MB), you can upload gzipped (<strong>*.gz</strong>) or compressed (<span id="boldtext">*.Z</span>) file for faster loading. </li> <p> <b>Reference: </b> Huanwang Yang, Vladimir Guranovic, Shuchismita Dutta, Zukang Feng, Helen M. Berman and John D. Westbrook (2004), Acta Cryst. D60, 1833-18399 <p><i>Questions, comments, and suggestions should be sent to <a href="mailto:deposit@deposit.rcsb.org">deposit@deposit.rcsb.org</a></i>.</p>  </div> <footer class="container_12 ui-corner-all"> <p>© <a href="http://www.rcsb.org">RCSB PDB</a></p> </footer> </div>  <iframe src="VERSION"></iframe> </body> </html>

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