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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">Molecular viewers</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/molecular-viewers?lang=ja" style="margin-right: 0.75em;">日本語</a><hr class="leftHR"></div><div property="articleBody" class="BLOG_BOX"> <style type="text/css"> </style> <h2>Molecular viewer support</h2> <p> In PDBj web site, we provide various molecular viewer pages. The available viewers for each web service is described below. </p> <table id="molecular_viewer"> <tbody><tr class="molecular_viewer_itemtitle"> <th rowspan="2">Services</th> <th colspan="4">Molecular Viewer</th> </tr> <tr class="molecular_viewer_itemtitle"> <th><a href="/help/jv">jV</a></th> <th><a href="/help/molmil">Molmil</a></th> <th>Jmol</th> <th>JSmol</th> </tr> <tr class="molecular_viewer_service"> <th><a href="/help/mine">PDBj Mine</a> (PDB data browser) asymmetric unit</th> <td>○</td> <td>○</td> <td>○</td> <td>○</td> </tr> <tr class="molecular_viewer_service"> <th><a href="/help/mine">PDBj Mine</a> (PDB data browser) biological unit</th> <td>−</td> <td>○</td> <td>−</td> <td>−</td> </tr> <tr class="molecular_viewer_service"> <th><a href="/help/chemie">Chemie</a> (chemical component browser)</th> <td>−</td> <td>○</td> <td>○</td> <td>○</td> </tr> <tr class="molecular_viewer_service"> <th>EDMap (Electron Density Map)</th> <td>−</td> <td>○</td> <td>−</td> <td>−</td> </tr> <tr class="molecular_viewer_service"> <th><a href="/help/sequence-navigator">Sequence Navigator</a> / <a href="/help/structure-navigator">Structure Navigator</a></th> <td>○</td> <td>○</td> <td>−</td> <td>−</td> </tr> <tr class="molecular_viewer_service"> <th><a href="/promode-elastic">Promode Elastic</a></th> <td>○</td> <td>○</td> <td>−</td> <td>−</td> </tr> <tr class="molecular_viewer_service"> <th><a href="/eF-site/">eF-site</a></th> <td>○</td> <td>○</td> <td>−</td> <td>−</td> </tr> <tr class="molecular_viewer_service"> <th><a href="/mom">Molecule of the Month</a></th> <td>−</td> <td>−</td> <td>○</td> <td>○</td> </tr> </tbody></table> <h3>Others</h3> <ul> <li> Note that the actual performance will vary depending on the molecular viewer, web browser and system specifications. </li> <li> Due to a recent revision of the <b>Google Chrome</b> or <b>Firefox</b> web browsers, the outdated plugin system used by Java is no longer supported and thus Java no longer works. So <b>molecular viewer pages with jV and Jmol are not available on Chrome or Firefox</b>. Please use Molmil/JSmol viewers instead. </li> <li> In case Java could not be detected, "NA" is shown for jV or Jmol viewer links.  To test whether you have Java installed and enabled, please visit our <a href="/browser-support">browser support test page</a> to test whether your browser supports Java. </li> <li> The <b>Jmol page doesn't support Mac OS 10.6</b>. Please refer another molecular viewer page such as JSmol page. </li> </ul> <h2 id="post_mine_au">Mine <a href="/help/about-aubu#asym_unit">Asymmetric Unit</a></h2> <ul> <li>Static images: <ul> <li>The images were created using <b>Molmil</b>.</li> </ul> </li> <li>Available viewers: <ul> <li> <b>jV</b> and <b>Jmol</b> are available on systems supporting Java Runtime Environment (JRE) when the molecular weight of the structure is less than 1.25MD. On non-mobile systems, such as <a href="http://en.wikipedia.org/wiki/IOS" rel="nofollow noopener" target="_blank">iOS</a> and <a href="http://en.wikipedia.org/wiki/Android_(operating_system)" rel="nofollow noopener" target="_blank">Android</a>, these viewers are not available because they don't have support for Java applets. </li><li> <b>Molmil</b> is available on systems which support <a href="http://en.wikipedia.org/wiki/WebGL" rel="nofollow noopener" target="_blank">webGL</a> and the (compressed) PDBx/mmCIF file is less than 20MB. On 64 bits browsers (excluding Chrome due to limitations of Chrome's JavaScript engine), the limit is higher at 100MB. Note that to load this type of large structures, a huge amount of memory is required (> 8GB). </li><li> <b>JSmol</b> is only available when the (compressed) PDBx/mmCIF filesize is less than 1MB due to performance reasons. </li> </ul> </li> </ul> <h2 id="post_mine_bu">Mine <a href="/help/about-aubu#bio_unit">Biological Unit</a></h2> <ul> <li>Static images: <ul> <li>The images were created using <b>Molmil</b>.</li> <li>Molmil's coarse surface was inspired by UCSF Chimera's Multiscale model<sup><a href="/help/molecular-viewers#note1">*1)</a></sup>. </li> </ul> </li> <li>Available viewers are <b>jV</b> and <b>Molmil</b>. System requirements about jV and Molmil are same as Mine Asymmetric unit. </li> </ul> <hr> <p id="note1"> *1) Software extensions to UCSF chimera for interactive visualization of large molecular assemblies.<br> Goddard, T.D., Huang, C.C., Ferrin, T.E. <em>Structure</em><b> 13</b>: 473-482 (2005) <a href="http://dx.doi.org/10.1016/j.str.2005.01.006" rel="nofollow noopener" target="_blank">[doi:10.1016/j.str.2005.01.006]</a> </p> </div><div style="margin-left: 3em; padding-bottom: 1.25em;"><hr class="leftHR"><div style="font-size: 0.75em;"><span property="datePublished">Created: 2020-09-25</span> <span style="color: #BFBFBF;">(last edited: more than 1 year ago)</span><span style="display: none;" property="dateModified">2020-09-25</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" href="/contact">Contact us</a><a title="Terms and Conditions" href="/info/terms-conditions">Terms and 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