PDB-IHM

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margin-right: 10px;" ><img src="/images/search.svg" alt="search" /></button> </form>   <p class="my-2"><a href="#" style="color:#FFF;" data-toggle="modal" data-target="#exampleModalCenter"><small>Search Tips</small></a></p>  <div class="modal fade" id="exampleModalCenter" tabindex="-1" role="dialog" aria-labelledby="exampleModalCenterTitle" aria-hidden="true"> <div class="modal-dialog modal-dialog-centered" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="exampleModalLongTitle">Search Tips</h5> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body"> <h6 style="color: #669966;"><b>Keyword Search</b></h6> <p>Search can be carried out using keywords such as</p> <ul> <li>macromolecular names (e.g., Exosome, p53)</li> <li>accession codes (e.g., PDBDEV_00000012, PDBDEV_00000014)</li> <li>experimental methods used (e.g., NMR, 3DEM, Crosslinking-MS)</li> <li>author names (e.g., Sali, Bonvin)</li> <li>software used (e.g., IMP, HADDOCK, ROSETTA)</li> </ul> <hr/> <h6 style="color: #669966;"><b>Boolean Search</b></h6> <p>Boolean operators are supported. </p> <ul> <li> AND (e.g., Kim AND Crosslinking-MS) </li> <li> OR (e.g., IMP OR HADDOCK) </li> <li> NOT (e.g., ROSETTA NOT Crosslinking-MS) </li> </ul> <hr/> <h6 style="color: #669966;"><b>Wild Card</b></h6> <p>Wild card symbol can be used to handle truncations. </p> <ul> <li> nup* can be used to search for all keywords that start with the phrase 'nup' (e.g., nup82, nup84, nup133). </li> <li> *trans* can be used to search for all keywords that contain the phrase 'trans' (e.g., methyltransferase, transcription). </li> <li> *some can be used to search for all keywords that end with the phrase 'some' (e.g., BBSome, exosome, nucleosome, proteasome). </li> </ul> <hr/> <h6 style="color: #669966;"><b>Phrase Search</b></h6> <p>Search for exact phrases can be carried out using single quotes (e.g., 'Nucleotide excision repair complex'). </p> <hr/> <h6 style="color: #669966;"><b>Attribute Search</b></h6> <p>Search for specific attributes defined in PDBx/mmCIF and IHM dictionaries can be carried out as follows. </p> <ul> <li>entry.id:*28</li> <li>entry.id:PDBDEV_00000012</li> <li>ihm_cross_link_list.linker_type:CYS</li> </ul> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div>  </div> </nav> <div class="card-body">  <div class="row"> <div class="col-sm-7">  <div class="card-header" style="background-color: #FFF; border:none;"> <br/> <h2 style="margin-left:50px;">Deposit Structures to PDB-IHM</h2> <br/> <br/> <div class="alert alert-primary" role="alert" style="margin-left:50px;"> <b>To submit a new structure, please visit the new <a href="https://data.pdb-ihm.org"><b>PDB-IHM Deposition and Data Harvesting System</b></a>.</b> </div> <br/> <p align="justify" style="margin-left:50px;">The <a href="https://data.pdb-ihm.org"><b>Data Harvesting System</b></a> provides a web interface for depositors to assemble all the information required for archiving integrative structures in PDB-IHM and to generate a compliant mmCIF file. A <a href="https://docs.google.com/document/d/1CM8-6PYqI0DvETeQEfoUpSFZ8BhLrvYnihLSK8ghVcI/"><b>User Guide</b></a> has been created with documentation regarding creating accounts and submitting data. Users are encouraged to provide any feedback via email to <a href="mailto:helpdesk@pdb-ihm.org"><b>helpdesk@pdb-ihm.org</b></a>.</p> <br> <p align="justify" style="margin-left:50px;">The old system has been deprecated as of June 3rd, 2022.</p> <br> <div class="alert alert-primary" role="alert" style="margin-left:50px;"> <b>PDB-IHM accepts structures determined using integrative modeling methods</b> </div> <br> <p align="justify" style="margin-left:50px;">Please note that experimental structures determined using X-ray crystallography or NMR spectroscopy or Electron microscopy should be deposited through the wwPDB <a href="https://deposit-2.wwpdb.org/deposition/"><b>OneDep</b></a> system.</p> <p align="justify" style="margin-left:50px;">Purely computational models obtained using homology modeling or <i> ab initio </i> methods should be deposited in the <a href="https://www.modelarchive.org"><b>ModelArchive</b></a>.</p> <br> <br/> <br/> <br/> <br/> <br/> </div> </div> </div>  </div>  <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="/color:#FFF; background-color: rgba(102,153,102, 0.5); ; padding-top: 10px; padding-bottom: 2px;"> <div class="col-sm-6" style="padding-top: 10px; padding-bottom: 10px;"> <a href="http://www.wwpdb.org/" target="_blank"> <img src="/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"/></a> </div>  <div class="col-sm-6"> <div class="float-right text-right"> <p style="margin-bottom: 0px; margin-right: 0px;color: #000"> Supported by<br />NSF, DOE, NIH</p> </div> </div> </div> <div class="row" style="color:#FFF; background-color: #669966; padding-top: 3px; padding-bottom: 8px;">  </div> </div> </div> </footer> <script> $.get(function(data){ $("#homequery").typeahead({ source: data, items: 8, minLength: 1, delay: 60, autoSelect: true, }); },'json'); $('#btnSearch').on('click', function () { var url; var searchInput = $('#homequery').val(); //if (searchInput) { url = "solrsearch.html?query=" + searchInput; window.open(url); } //minimum of 3 characters var regex0 = new RegExp ( "(.){3,}" ); var results0 = regex0.exec( searchInput ); if (results0 !== null) { //test for an PDB-IHM id with or without "PDBDEV" prefix var regex1 = new RegExp ( "^[pP][dD][bB][dD][eE][vV]_[0-9]{8,}$" ); var regex2 = new RegExp ( "^[0-9]{8,}$" ); //pure number 8+ digits var results1 = regex1.exec( searchInput ); var results2 = regex2.exec( searchInput ); if (results1 !== null) { url = "entry.html?PDBDEV_" + searchInput.slice(7); window.open(url); } else if (results2 !== null) { url = "entry.html?PDBDEV_" + searchInput; window.open(url); } else { url = "solrsearch.html?query=" + searchInput; window.open(url); } } }); </script> </div> <script type="text/javascript" src="/js/jquery-1.11.2.min.js"></script> <script type="text/javascript" src="/js/validator.min.js"></script> <script type="text/javascript" src="/js/form-scripts.js"></script> </body> </html>

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PDB-IHM