PDB-IHM

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} .navbar-dark .navbar-nav .nav-link.disabled { color: rgba(255, 255, 255, 0.25); } .navbar-dark .navbar-text a:hover, .navbar-dark .navbar-text a:focus { color: #fff; } .nav .faq{ font-weight:bold; color: #fff; } .home-header { display: none; } </style> </head> <body style="background-color: #669966; "> <script type="text/javascript" src="/js/auto.js"></script> <style> .btn-round{ border-radius: 5px; } </style> <div class="container-fluid"> <div class="card" style="border: none; margin-bottom: 0px; margin-right: 10px; margin-left: 30px; "> <div class="float-left"><b><span id="siteid"></span></b></div>  <div class="card-body" style="padding: 0px 0px;background-color: rgba(102,153,102, 0.5); " > <div class="row"> <div class=" col-sm-9" style="margin-left: 0px;"><a href="/index.html"> <img src="/images/logon.png" class="float-left" alt="PDBIHM.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" /> <p><h1 style="margin-left: 0px; color: #003366;">PDB-IHM</h1><h5 class="float-left" style="color: #003366;">System for Archiving Integrative Structures</h5></p>  </a> </div> <div class="col-sm-3 d-flex align-items-end" style="margin-top: 0px;"><h6 onload="autofunction()" id="auto" class="home-header ml-auto" style="margin-right:27px; margin-top:75px; color:#003366"><b><small></small></b></h6></div> </div> </div> <nav class="navbar navbar-expand-xl 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 mr-4"><a class="nav-link" href="/index.html"><span class="home">Home</span></a></li> <li class="nav-item mr-4"><a class="nav-link" href="/about.html"><span class="about">About</span></a></li> <li class="nav-item mr-4"><a class="nav-link" href="/deposit.html"><span class="deposit">Deposit</span></a></li> <li class="nav-item mr-4"><a class="nav-link" href="/contact.html"><span class="contact">Contact</span></a></li> <li class="nav-item"><a class="nav-link" href="/faq.html"><span class="faq">FAQ</span></a></li>  </ul> <form class="form-inline my-2 my-lg-0"> <div class="input-group"> <input type="button" onclick="location.href='/solrsearch.html?query=*:*';" id="allentries" class=" btn-round mr-sm-2" style="background-color: #669966;color:#FFF;border:none;cursor: pointer;" value="Browse Structures" /> <div class="input-group-btn"> <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="Keyword Search (e.g., NPC AND 3DEM)" aria-label="Search PDB-IHM" style="width:325px;"> </div> </div> <button id="btnSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" style="background-color: #669966; 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-lg-12">  <div class="card-header" style="background-color: #FFF; border:none;"> <h2>Frequently Asked Questions</h2> <br/>  <div class="accordion" id="accordionExample"> <div class="card"> <div class="card-header" id="headingOne"> <h2 class="mb-0"> <button class="btn btn-link" type="button" data-toggle="collapse" data-target="#collapseOne" aria-expanded="true" aria-controls="collapseOne"> <div style="white-space:normal" align="justify"><b>1. What kind of models can be deposited to PDB-IHM?</b></div> </button> </h2> </div> <div id="collapseOne" class="collapse" aria-labelledby="headingOne" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">We currently accept integrative or hybrid models that follow the specifications defined in the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a>. The dictionary is a modular extension of the <a href="http://mmcif.wwpdb.org/">PDBx/mmCIF</a> dictionary used in the <a href="http://www.wwpdb.org/">PDB</a> archive. This dictionary supports multi-scale, multi-state, and ordered ensembles of macromolecular assemblies along with definitions for spatial restraints derived from a variety of experimental techniques.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingTwo"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTwo" aria-expanded="false" aria-controls="collapseTwo"> <div style="white-space:normal" align="justify"><b>2. I have an experimental model determined using X-ray crystallography / NMR spectroscopy / Electron microscopy. Can I deposit my structure in PDB-IHM?</b></div> </button> </h2> </div> <div id="collapseTwo" class="collapse" aria-labelledby="headingTwo" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">No. 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/">OneDep system.</a></p></div> </div> </div> <div class="card"> <div class="card-header" id="headingThree"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseThree" aria-expanded="false" aria-controls="collapseThree"> <div style="white-space:normal" align="justify"><b>3. I have a computational model obtained using homology modeling or ab initio methods. Can I deposit my structure in PDB-IHM?</b></div> </button> </h2> </div> <div id="collapseThree" class="collapse" aria-labelledby="headingThree" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">No. Purely computational models obtained using homology modeling or ab initio methods should be deposited in the <a href="https://www.modelarchive.org/">ModelArchive</a>.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFour"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFour" aria-expanded="false" aria-controls="collapseFour"> <div style="white-space:normal" align="justify"><b>4. Where do I deposit the experimental data based on which my structure was determined?</b></div> </button> </h2> </div> <div id="collapseFour" class="collapse" aria-labelledby="headingFour" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">The integrative / hybrid models and the associated spatial restraints should be deposited here at PDB-IHM and should comply with the definitions in the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary.</a></p> <p align="justify">The primary experimental data from which the spatial restraints are derived should be deposited in the corresponding experimental data repository. The following guidelines may be followed for depositing primary experimental data.<p/> <ul style="color: #000; margin-left: 2em;" > <li>NMR data (not accepted by the wwPDB <a href="https://deposit-2.wwpdb.org/deposition/">OneDep system</a>) can be deposited at <a href="https://bmrb.io/">BMRB.</a></li> <li>3DEM map data can be deposited at <a href="https://www.ebi.ac.uk/pdbe/emdb/">EMDB.</a></li> <li>EM micrographs and 2DEM class averages can be deposited at <a href="https://www.ebi.ac.uk/pdbe/emdb/empiar/">EMPIAR.</a></li> <li>SAS data can be deposited at <a href="https://www.sasbdb.org/">SASBDB.</a></li> <li>Proteomics data can be deposited at the <a href="http://www.proteomexchange.org/">ProteomeXchange Consortium.</a></li> </ul> <p align="justify">The accession codes pertaining to these depositions should be included with the structure deposited in PDB-IHM.</p> <p align="justify">In case there is no primary data repository corresponding to the experimental data used in the modeling, then the data should be referenced using a <a href="https://www.doi.org">Digital Object Identifier (DOI)</a>. DOIs may be obtained from any provider. <a href="https://zenodo.org/">Zenodo</a> is a DOI provider frequently used by PDB-IHM depositors.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFive" aria-expanded="false" aria-controls="collapseFive"> <div style="white-space:normal" align="justify"><b>5. Are there any specific requirements for uploading files?</b></div> </button> </h2> </div> <div id="collapseFive" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">The model file has to be in a format compliant with the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a>. We do not accept depositions in PDB format.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingSix"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseSix" aria-expanded="false" aria-controls="collapseSix"> <div style="white-space:normal" align="justify"><b>6. Are there any software programs that support IHMCIF?</b></div> </button> </h2> </div> <div id="collapseSix" class="collapse" aria-labelledby="headingSix" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">We provide a standalone software library called <a href="https://github.com/ihmwg/python-ihm">python-ihm</a> that supports the new <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a>. The library can be used to read and write data files compliant with the dictionary. Please see the <a href="https://python-ihm.readthedocs.io/en/latest/">documentation</a> or some <a href="https://github.com/ihmwg/python-ihm/tree/master/examples">worked examples</a> for more details.<p> <p align="justify">Integrative modeling software such as <a href="https://integrativemodeling.org/">IMP</a> support the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a>. Work is in progress for other integrative modeling software such as <a href="https://rascar.science.uu.nl/haddock2.4/">HADDOCK</a> to support the dictionary.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingSeven"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseSeven" aria-expanded="false" aria-controls="collapseSeven"> <div style="white-space:normal" align="justify"><b>7. Can these models be viewed using existing molecular visualization tools?</b></div> </button> </h2> </div> <div id="collapseSeven" class="collapse" aria-labelledby="headingSeven" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">The structures in PDB-IHM can be downloaded and visualized using the <a href="https://www.rbvi.ucsf.edu/chimerax/">UCSF ChimeraX</a> visualization software, which provides built-in support for the new IHM data dictionary. Please use the daily build for the most up-to-date visualization and use the command line option "format ihm" to visualize multi-scale structures. For more details, please refer to the <a href="/allnews.html#collapseOne">news item</a> related to ChimeraX.</p> <p align="justify"> Integrative structures can also be visualized using the <a href="https://molstar.org/viewer/">Molstar viewer</a>. <a href="https://molstar.org/">Molstar</a> is an open collaboration started by <a href="https://ebi.ac.uk/pdbe/">PDBe</a> and <a href="https://www.rcsb.org">RCSB PDB</a> to provide a technology stack for data delivery and analysis tools of macromolecules. <a href="https://molstar.org/viewer/">Molstar viewer</a> is now embedded within the PDB-IHM website and structures in PDB-IHM can be visualized through <a href="https://molstar.org/">Molstar</a> from the individual entry pages. Molstar can visualize atomic as well as multi-scale structures. For more details, please refer to the <a href="/allnews.html#collapseFour">news item</a> related to Molstar.</p> <p align="justify"> Work is in progress to support the visualization of integrative structures using other molecular visualization tools. We recommend depositors to upload an image of their modeled structure along with the deposition.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingEight"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseEight" aria-expanded="false" aria-controls="collapseEight"> <div style="white-space:normal" align="justify"><b>8. How do I deposit a new structure?</b></div> </button> </h2> </div> <div id="collapseEight" class="collapse" aria-labelledby="headingEight" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">Please visit the <a href="/deposit.html">PDB-IHM deposition page</a> for instructions on depositing new structures.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingNine"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseNine" aria-expanded="false" aria-controls="collapseNine"> <div style="white-space:normal" align="justify"><b>9. How do I delete a deposited structure?</b></div> </buttn> </h2> </div> <div id="collapseNine" class="collapse" aria-labelledby="headingNine" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">Structures that have been released cannot be deleted. Users can delete entries that have not been submitted. For deleting other depositions, users can <a href="/contact.html">contact</a> or <a href="mailto:helpdesk@pdb-ihm.org">email</a> us.</P> </div> </div> </div> <div class="card"> <div class="card-header" id="headingTen"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTen" aria-expanded="false" aria-controls="collapseTen"> <div style="white-space:normal" align="justify"><b>10. How do I contact PDB-IHM for deposition related issues?</b></div> </button> </h2> </div> <div id="collapseTen" class="collapse" aria-labelledby="headingTen" data-parent="#accordionExample"> <div class="card-body"> Users can contact us via email (<a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a>). Please visit our <a href="/contact.html">contact</a> page for more information.</div> </div> </div> <div class="card"> <div class="card-header" id="headingEleven"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseEleven" aria-expanded="false" aria-controls="collapseEleven"> <b>11. How do I cite PDB-IHM?</b> </button> </h2> </div> <div id="collapseEleven" class="collapse" aria-labelledby="headingEleven" data-parent="#accordionExample"> <div class="card-body"> <p>To cite PDB-IHM, please use one of the following references:</p> <ul> <li><p align="justify">Vallat B et al., Acta Cryst. 2021; D77: 1486-1496, <a href="https://doi.org/10.1107/S2059798321010871">doi: 10.1107/S2059798321010871</a></p></li> <li><p align="justify">Vallat B et al., Structure. 2018 Jun; 26(6):894-904, <a href="https://doi.org/10.1016/j.str.2018.03.011">doi: 10.1016/j.str.2018.03.011</a>.</p></li> </ul> <p align="justify">To cite a structure from PDB-IHM, please use the primary citation of the structure and the PDB/PDB-IHM accession code. </p> </div> </div> <div class="card"> <div class="card-header" id="headingTwelve"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTwelve" aria-expanded="false" aria-controls="collapseTwelve"> <b>12. Can entries be kept on embargo until publication?</b> </button> </h2> </div> <div id="collapseTwelve" class="collapse" aria-labelledby="headingTwelve" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">Yes. Once the deposition is processed, an accession code is issued, after which the entry can either be released or kept on hold. Following <a href="https://wwpdb.org/documentation/policy">wwPDB policies</a>, entries can be placed on hold for a maximum period of one year from the date of deposition. If an entry remains unreleased at the end of the hold period, it must either be released or withdrawn.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingThirteen"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseThirteen" aria-expanded="false" aria-controls="collapseThirteen"> <b>13. How are new PDB-IHM entries released?</b> </button> </h2> </div> <div id="collapseThirteen" class="collapse" aria-labelledby="headingThirteen" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">PDB-IHM entries are updated along with the PDB archive each week on or about Wednesday 00:00 UTC (Coordinated Universal Time) with new releases, modified entries, and updated status information. Updates are prepared on the previous Friday. Citation updates and release requests should be sent to <a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a> by noon ET on the preceding Thursday to be included in the current release cycle. Entries that are complete and only require citation updates will be included in the current release; entries that require additional curation before release and requests received after an update has been packaged will appear with the following release cycle. The files in the FTP archive have the Thursday timestamp of the internal update packaging.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFourteen"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFourteen" aria-expanded="false" aria-controls="collapseFourteen"> <b>14. How do I generate a compliant mmCIF file from the models and data that I have?</b> </button> </h2> </div> <div id="collapseFourteen" class="collapse" aria-labelledby="headingFourteen" data-parent="#accordionExample"> <div class="card-body"> <p align="justify">We have developed a new <a href="https://data.pdb-ihm.org">Data Harvesting System</a> that provides a web interface for depositors to assemble all the information required for archiving integrative structures in PDB-IHM and to create a compliant mmCIF file. This includes the submission of integrative structures, associated spatial restraints and starting models used, modeling protocols and metadata information (citations, authors, software, data in external repositories, reference sequence information etc.). </p> <p align="justify">The data harvesting system provides an automated mechanism for collecting diverse and heterogeneous types of integrative structures and restraint data. The system has been developed using the <a href="https://www.isi.edu/isr/research-areas/the-deriva-platform/">DERIVA</a> scientific asset management platform and is based on the definitions in the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a> and the parent <a href="https://mmcif.wwpdb.org">PDBx/mmCIF</a> dictionary. </p> <p align="justify">A <a href="https://docs.google.com/document/d/1CM8-6PYqI0DvETeQEfoUpSFZ8BhLrvYnihLSK8ghVcI/">User Guide</a> has been created with documentation regarding creating accounts and submitting data. </p> <p align="justify">Users are encouraged to provide any feedback via email to <a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a>.</p> </div> </div> </div> </div> </div> </div> </div> </div>  </div>  <script> function openAnchorAccordion() { if (window.location.hash) { var jQuerytarget = jQuery('body').find(window.location.hash); if (jQuerytarget.hasClass('collapse')) { var jQuerytargetAccordion = jQuerytarget.find('.collapse'); jQuerytarget.collapse('show'); } } } openAnchorAccordion(); jQuery("body").on("click", "a", openAnchorAccordion); </script> <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> </body> </html>

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