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Search</a><a title="PDBj Omni Search Help" href="/help/omni-search">Search help</a></div></div></header><div><main id=""><div class="sNP" typeof="Article"><h1 property="name headline">FAQ</h1><div><div class="OGhover opacityTransition2 _langList_" style="margin-left: 3em;"><span>This page is also available in: </span><a title="日本語" href="/help/faq?lang=ja" style="margin-right: 0.75em;">日本語</a><hr class="leftHR"></div><div property="articleBody" class="BLOG_BOX"> <style> a { text-decoration: none; } a:hover { text-decoration: underline; } </style> <h2>[Frequently Asked Questions]</h2> <h3>1. Update & download of PDB data</h3> <ul> <li> <a href="/help/faq_data01"> 1-1) When are PDB entries released or updated? Can I download exactly the same PDB data from RCSB PDB, PDBe or PDBj? 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The number is specified as a percentage.</p> <pre class="codeQuoteBox">zoom 130 </pre> <p>After that, save the image by clicking on [File] > [Save] > [(file format)].</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="EM_1"> <h4>4-8) EM: I have a question about EM Navigator. Who do I contact?</h4> <p>A) Please see the <a href="/emnavi/emnavi_doc.php?&lang=en">FAQ page of EM Navigator</a>. If you do not find the answer to your question, please feel free to <a href="/contact"><b>contact us</b></a>. </p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="EM_2"> <h4>4-9) EM: How do I reproduce a map from a session file of EM Navigator?</h4> <p>A) Please download a session file and a map file from EM Navigator's Detail page. Please put the decompressed map file and the session file in the same directory. Restore the session using UCSF Chimera and the atomic model and the map will be displayed. 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We will send the next Newsletter to your new address.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="other_2"> <h4>5-2) Do you have a reference regarding PDB XML format and various services?</h4> <p>A) Please refer to the following reference on XML format.</p> <p><b>PDBML: The representation of archival macromolecular structure data in XML</b><br> Westbrook, J.D., Ito, N., Nakamura, H., Henrick, K., Berman, H.M.<br> <em>Bioinformatics</em> <b>21</b> (7): 98 (2005) <a href="http://www.ncbi.nlm.nih.gov/pubmed/15509603" rel="nofollow noopener" target="_blank">[PubMed]</a> <a href="http://dx.doi.org/10.1093/bioinformatics/bti082" rel="nofollow noopener" target="_blank">[doi:10.1093/bioinformatics/bti082]</a></p> <p>Other publications are listed on the <a href="/info/publications"><b>Publication</b></a> page.</p><a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="other_3"> <h4>5-3) Where do I get XML schema files for PDB XML data?</h4> <p>A) The XML Schema files for PDBML and PDBMLplus data are available on the following pages:</p> <p><b>PDBML:</b><br> <a href="/schema/pdbx-v40.xsd">http://pdbj.org/schema/pdbx-v40.xsd</a> / <a href="/schema/pdbx-v42.xsd">http://pdbj.org/schema/pdbx-v42.xsd</a> </p> <p><b>PDBMLplus:</b><br> <a href="/help/pdbmlplus-schema">PDBMLplus schema</a> page</p> <p>See <a href="/help/data-format">PDBj Help page</a> for the details of the data format, PDBML and PDBMLplus.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="other_4"> <h4>5-4) How do I link to a Structure Summary page of PDBj Mine for a PDB ID?</h4> <p>A) The correct syntax for linking to a Structure Summary page for a structure by PDB ID on the site is as follows (example 1NIH):</p> <ul>  <li>general URL (language is automatically determined)<br> <a href="/pdb/1nih"><b>http://pdbj.org/pdb/1nih</b></a></li> <li>Japanese page<br> <a href="/pdbj/1nih"><b>http://pdbj.org/pdb<span style="color: red;">j</span>/1nih</b></a></li> </ul> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="other_5"> <h4>5-5) Why is "j" written in lowercase while "J" of Japan is written in uppercase?</h4> <p>A) <span class="bold">PDBj</span> ( <span class="underline">P</span> rotein <span class="underline">D</span> ata <span class="underline">B</span> ank <span class="underline">J</span> apan) maintains a centralized <span class="bold">PDB</span> archive of macromolecular structures as a member of the wwPDB collaborating with the RCSB, the BMRB in USA and the PDBe in EU.</p> <p>To emphasize <span class="bold">PDB</span> which is written in uppercase, we write a site identification character, the last <span class="bold">j</span>, in lowercase.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="other_6"> <h4>5-6) How can I uncompress gz file(.gz) on Windows? 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Please see <a href="http://ef-site.hgc.jp/wiki/jV/index.php/Installation_of_jV3" rel="nofollow noopener" target="_blank">Installation of jV3</a> page.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="trouble_3"> <h4>6-3) jV: I have a problem displaying a PDB structure using PDBjViewer. What can I do?</h4> <p>A) PDBj Viewer is the old version of jV. Please install <a href="http://ef-site.hgc.jp/wiki/jV/index.php/Installation_of_jV3" rel="nofollow noopener" target="_blank">the latest version of jV</a>.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="trouble_4"> <h4>6-4) jV: I encounter an error when using jV applet to view a structure.</h4> <p>A) When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux, jV applet and applet-launcher fails to start up with the following error.</p> <pre class="codeQuoteBox">Error:java.io.IOException:Cannot find certificates for JNLP AppletLauncher class </pre> <p>Please use JRE6 Update17 (1.6.0_17) or later.</p> <p>If you have any other viewing problems, please refer to <a href="http://ef-site.hgc.jp/wiki/jV/index.php/Trouble_shooting" rel="nofollow noopener" target="_blank">the jV wiki Trouble shooting page</a>.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="trouble_5"> <h4>6-5) jV: I have a problem in installing jV and/or displaying a PDB structure using jV.</h4> <p>A) If you have installation or viewing problems, please refer to <a href="http://ef-site.hgc.jp/wiki/jV/index.php/Trouble_shooting" rel="nofollow noopener" target="_blank">the jV wiki Trouble shooting page</a>.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div>  <div id="pdb_1"> <h4>7-1) Do you have documentation for the PDB file format?</h4> <p>A) Documentation describing the PDB file format and annotation policies is available from the wwPDB at <a href="http://www.wwpdb.org/docs.html" rel="nofollow noopener" target="_blank">http://www.wwpdb.org/docs.html</a>.<br> Please refer to the newest version of thePDB file format - Contents Guide.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="pdb_2"> <h4>7-2) I want to change my PDB entry but do not know the contact e-mail address. What can I do?</h4> <p>A) Please contact the PDBj deposition and annotation staff using <a href="/contact">this form</a>.<br> Be sure to include the PDB ID or RCSB ID in the subject.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="pdb_3"> <h4>7-3) Can I complete a deposition over a few days? For how long is my incomplete deposition session saved?</h4> <p>A) Yes, you can complete depositing a structure using wwPDB deposition system over a few days.<br> In fact, your incomplete session is saved for a limit of 6 months from when it is first started. </p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="pdb_4"> <h4>7-4) When will an HPUB structure be released? The primary citation has been published.</h4> <p>A) We would appreciate it if you could provide the publication information from the <a href="/contact"><b>Contact Us</b></a> page.<br> The structure will be released the next Wednesday at 9 a.m.(JST) at the earliest, otherwise, on the Wednesday of the following week.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div>  <div id="pdb_6"> <h4>7-6) What is the rule for assigning chain IDs? How are upper case letters, lower case letters and numbers used?</h4> <p>A) Please refer to <a href="http://www.wwpdb.org/procedure.html" rel="nofollow noopener" target="_blank">4 Chain ID assignment</a> of Processing Procedures manual at <a href="http://www.wwpdb.org/docs.html" rel="nofollow noopener" target="_blank">http://www.wwpdb.org/docs.html</a>.</p> <p>Upper case letters and numbers should be used first for chain IDs. Lower case letters should be used only after all upper letters and numbers 0-9 have been used. In this way, a maximum of 62 chains can be included in the PDB entry. Other symbols should never be used for chain IDs.</p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div> <div id="pdb_7"> <h4>7-7) Can I release my PDB entry (deposited as HPUB/HOLD) right away?</h4> <p> A) PDB entries can always be released at depositors request once annotation is complete . </p><p> Please contact the PDBj deposition and annotation staff using <a href="/contact">this form</a>.<br> Be sure to include the PDB ID or RCSB ID in the subject. </p> <a href="/help/faq#top">[Back to Questions]</a> <hr> </div></div> </div><div style="margin-left: 3em; padding-bottom: 1.25em;"><hr class="leftHR"><div style="font-size: 0.75em;"><span property="datePublished">Created: 2020-11-02</span> <span style="color: #BFBFBF;">(last edited: more than 1 year ago)</span><span style="display: none;" property="dateModified">2020-11-02</span></div></div></div></div></main><aside id=""></aside><footer><div class="sPlane"><div><a title="Help" href="/help">Help</a><a title="Contact us" 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