Yorodumi related documents

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onclick="_pmov.size(-50)"><</button><button class="sizebtn" onclick="_pmov.size(0)"><div class="sizebox_ss"></div></button><button class="sizebtn" onclick="_pmov.size(1)"><div class="sizebox_s"></div></button><button class="sizebtn" onclick="_pmov.size(2)"><div class="sizebox_m"></div></button><button class="sizebtn" onclick="_pmov.size(3)"><div class="sizebox_l"></div></button><button class="sizebtn" onclick="_pmov.size(4)"><div class="sizebox_ll"></div></button><button onclick="_pmov.size(50)">></button><li><button onclick="_pmov.tile()">tile</button><li><button onclick="_pmov.play(1)"><img src="img/lk-play.gif" class="lkicon">Play</button><button onclick="_pmov.play()"><img src="img/lk-pause.gif" class="lkicon">Pause</button><li>Orientation:<table class="noborder"><tr><td><td><button onclick="_pmov.ori2('top')"><img src="img/top.gif" decoding="async"></button><td><tr><td><button onclick="_pmov.ori2('left')"><img src="img/left.gif" decoding="async"></button><td><button onclick="_pmov.ori2('front')"><img src="img/front.gif" decoding="async"></button><td><button onclick="_pmov.ori2('right')"><img src="img/right.gif" decoding="async"></button><tr><td><button onclick="_pmov.ori2('back')"><img src="img/back.gif" decoding="async"></button><td><button onclick="_pmov.ori2('bottom')"><img src="img/bottom.gif" decoding="async"></button><td><button onclick="_pmov.ori2('cut')"><img src="img/cut.gif" decoding="async"></button></table></ul>" class="poptrg"><img src="img/lk-opt.gif" class="lkicon">Controller</span></div></div><div id="vwctrl" class="hide"><h2 id="h_page_menu" onclick="_hdiv.oc('page_menu')"><div id="oc_btn_page_menu" class="oc_btn">-</div><img src="img/lk-view.gif" class="lkicon">Structure viewers</h2><div id="oc_div_page_menu" class="oc_div lev2"><ul id="vwlist"></ul></div><h2 id="h_i34" onclick="_hdiv.oc('i34')"><div id="oc_btn_i34" class="oc_btn">+</div>Viewer log</h2><div id="oc_div_i34" class="oc_div lev2 hide"><div id="cmdhist"></div></div></div><h2 id="h_page_menu" onclick="_hdiv.oc('page_menu')"><div id="oc_btn_page_menu" class="oc_btn">-</div>This page</h2><div id="oc_div_page_menu" class="oc_div lev2"><button onclick="_hdiv.all()">Show/hide all</button><span class="nw"><input type="checkbox" id="hdiv_exc"><label for="hdiv_exc">Exclusive</label></span><ul><li class="clickable" onclick="_hdiv.focus('i29')">Search & filter documents</li><li class="clickable" onclick="_hdiv.focus('i30')">News (10)</li><li class="clickable" onclick="_hdiv.focus('i31')">FAQ (3)</li><li class="clickable" onclick="_hdiv.focus('i32')">Information (15)</li><li class="clickable" onclick="_hdiv.focus('about')"><img src="img/lk-help.gif" class="lkicon">About Yorodumi Docs</li></ul></div><h2 id="h_i35" onclick="_hdiv.oc('i35')"><div id="oc_btn_i35" class="oc_btn">-</div>This web site</h2><div id="oc_div_i35" class="oc_div lev2"><ul><nav><li itemscope="itemscope" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="https://pdbj.org" itemprop="url" target="_blank"><img src="img/lk-pdbj.gif" class="lkicon"><span itemprop="title">PDBj</span></a></li><ul class="pankuzu"><ul><li itemscope="itemscope" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="quick.php" itemprop="url"><img src="img/lk-miru.gif" class="lkicon"><span itemprop="title">Yorodumi</span></a></li><ul><li><img src="img/lk-help.gif" decoding="async"><span itemprop="title">Yorodumi Docs</span></li></ul></ul></ul></nav><li><form class="topline" method="get" action="ysearch.php"><a href="ysearch.php" itemprop="url"><img src="img/lk-search.gif" class="lkicon"><span itemprop="title">Cross-search</span></a>: <input type="search" class="acomp" name="kw" list="acomp_kw" size="15"></form><li><a href="." itemprop="url"><img src="img/lk-emn.gif" class="lkicon"><span itemprop="title">EM Navigator</span></a> <span onclick="_pop.up(this)" data-pop="<ul><li><a href="esearch.php" itemprop="url"><img src="img/lk-search.gif" class="lkicon"><span itemprop="title">EMN Search</span></a><li><a href="stat.php" itemprop="url"><img src="img/lk-statistics.gif" class="lkicon"><span itemprop="title">EMN Statistics</span></a><li><a href="gallery.php" itemprop="url"><img src="img/lk-gallery.gif" class="lkicon"><span itemprop="title">EMN Gallery</span></a><li><a href="pap.php?em=1" itemprop="url"><img src="img/lk-article.gif" class="lkicon"><span itemprop="title">EMN Papers</span></a><li><a href="covid19.php" itemprop="url"><img src="img/lk-link.gif" class="lkicon"><span itemprop="title">Covid-19 info</span></a><li><a href="doc.php?tag=emn" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">About EM Navigator</span></a></ul>" class="poptrg"><i class="fa fa-plus-square large"></i></span><li><a href="quick.php" itemprop="url"><img src="img/lk-miru.gif" class="lkicon"><span itemprop="title">Yorodumi</span></a> <span onclick="_pop.up(this)" data-pop="<ul><li><a href="ysearch.php" itemprop="url"><img src="img/lk-search.gif" class="lkicon"><span itemprop="title">Yorodumi Search</span></a><li><a href="pap.php" itemprop="url"><img src="img/lk-article.gif" class="lkicon"><span itemprop="title">Yorodumi Papers</span></a><li><a href="taxo.php" itemprop="url"><img src="img/lk-taxo.gif" class="lkicon"><span itemprop="title">Yorodumi Species</span></a><li><a href="doc.php?tag=ym" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">About Yorodumi</span></a></ul>" class="poptrg"><i class="fa fa-plus-square large"></i></span><li><a href="omo-search.php" itemprop="url"><img src="img/lk-omokage.gif" class="lkicon"><span itemprop="title">Omokage search</span></a> <span onclick="_pop.up(this)" data-pop="<ul><li><a href="doc.php?tag=omos" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">About Omokage search</span></a></ul>" class="poptrg"><i class="fa fa-plus-square large"></i></span><li><a href="doc.php" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title"></span></a> <span onclick="_pop.up(this)" data-pop="<ul><li><a href="doc.php?type=info" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">Help</span></a><li><a href="doc.php?type=faq" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">FAQ</span></a><li><a href="doc.php?type=news" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">News</span></a><li><a href="doc.php?tag=about" itemprop="url"><img src="img/lk-help.gif" class="lkicon"><span itemprop="title">Pages</span></a></ul>" class="poptrg"><i class="fa fa-plus-square large"></i></span></ul></div><h2 id="h_i36" onclick="_hdiv.oc('i36')"><div id="oc_btn_i36" class="oc_btn">-</div><img src="img/lk-opt.gif" class="lkicon">Options</h2><div id="oc_div_i36" class="oc_div lev2"><ul><li><b>[English]</b> <a href="/emnavi/doc.php?lang=ja&tag=ym">日本語</a><li>Structure viewers<ul><li>Molecule: <select class="menu_viewer_mol" onchange="_vw.select_defvw('mol',this)"><option value="molmil">Molmil</option><option value="jmol">Jmol/JSmol</option></select><li>EM map: <select class="menu_viewer_map" onchange="_vw.select_defvw('map',this)"><option value="sview">SurfView</option><option value="molmil">Molmil</option><option value="jmol">Jmol/JSmol</option></select></ul><li>Font size: <button class="sizebtn fsizebtn" id="fsize0" onclick="_fsize(0)"><div class="sizebox_ss"></div></button><button class="sizebtn fsizebtn" id="fsize1" onclick="_fsize(1)"><div class="sizebox_s"></div></button><button class="sizebtn fsizebtn" id="fsize2" onclick="_fsize(2)" disabled><div class="sizebox_m"></div></button><button class="sizebtn fsizebtn" id="fsize3" onclick="_fsize(3)"><div class="sizebox_l"></div></button><button class="sizebtn fsizebtn" id="fsize4" onclick="_fsize(4)"><div class="sizebox_ll"></div></button></ul></div></div></div></div><div id="mainbox"><header><div id="simple_top" class="clearfix"><div id="top_opt"><b>[English]</b> <a href="/emnavi/doc.php?lang=ja&tag=ym">日本語</a><br><button id="btn_menu_pop" onclick="_extcol.menu(1)"><img src="img/lk-menu.gif" class="lkicon">menu</button></div><span onclick="_pop.up(this)" data-pop="<ul><nav><li itemscope="itemscope" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="https://pdbj.org" itemprop="url" target="_blank"><img src="img/lk-pdbj.gif" class="lkicon"><span itemprop="title">PDBj</span></a></li><ul class="pankuzu"><ul><li itemscope="itemscope" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="quick.php" itemprop="url"><img src="img/lk-miru.gif" class="lkicon"><span itemprop="title">Yorodumi</span></a></li><ul><li><img src="img/lk-help.gif" decoding="async"><span itemprop="title">Yorodumi Docs</span></li></ul></ul></ul></nav><li><form class="topline" method="get" action="ysearch.php"><a href="ysearch.php" itemprop="url"><img src="img/lk-search.gif" class="lkicon"><span itemprop="title">Cross-search</span></a>: <input type="search" class="acomp" name="kw" list="acomp_kw" size="15"></form><li><a href="." itemprop="url"><img src="img/lk-emn.gif" class="lkicon"><span itemprop="title">EM Navigator</span></a> <span onclick="_pop.up(this)" data-pop="&lt;ul&gt;&lt;li&gt;&lt;a href=&quot;esearch.php&quot; itemprop=&quot;url&quot;&gt;&lt;img src=&quot;img/lk-search.gif&quot; class=&quot;lkicon&quot;&gt;&lt;span itemprop=&quot;title&quot;&gt;EMN Search&lt;/span&gt;&lt;/a&gt;&lt;li&gt;&lt;a href=&quot;stat.php&quot; itemprop=&quot;url&quot;&gt;&lt;img src=&quot;img/lk-statistics.gif&quot; class=&quot;lkicon&quot;&gt;&lt;span itemprop=&quot;title&quot;&gt;EMN Statistics&lt;/span&gt;&lt;/a&gt;&lt;li&gt;&lt;a href=&quot;gallery.php&quot; itemprop=&quot;url&quot;&gt;&lt;img src=&quot;img/lk-gallery.gif&quot; class=&quot;lkicon&quot;&gt;&lt;span itemprop=&quot;title&quot;&gt;EMN Gallery&lt;/span&gt;&lt;/a&gt;&lt;li&gt;&lt;a href=&quot;pap.php?em=1&quot; 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Only RNA coordinates are used for the orientation.</li></ul><li>Color:</li><ul class="doc_ul"><li>monomer AUs: by N->C (blue->red) rainbow</li><li>BUs of monomer AUs: by "color molecule" (Jmol's coloring)</li><li>multimer AUs and thier BUs (including monomer BUs): by "color chain". For this coloring, Jmol uses not a rainbow color but the colors determined by the chain-ID.</li></ul><li>Problems:</li><ul class="doc_ul"><li>BU models are generated by Jmol's system. It works well for the most data, but there are some exception.</li><li>Checking and fixing processes of the many (>200,000) images are in progress. There are still some wrong images.</li></ul></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=how_to_make_emdbimg&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.?</span></p><p class="small"><b>External links</b>:<a href="https://jmol.sourceforge.net/" target="_blank"><img src="img/lk-link.gif" class="lkicon">Jmol: an open-source Java viewer for chemical structures in 3D</a></p></div></div><h1 id="h_i32" onclick="_hdiv.oc('i32')"><div id="oc_btn_i32" class="oc_btn">-</div>Information (15)</h1><div id="oc_div_i32" class="oc_div lev1"><button onclick="_hdiv.all2(this)">Show/hide all</button><h2 id="h_i14" onclick="_hdiv.oc('i14')"><div id="oc_btn_i14" class="oc_btn">+</div>Yorodumi</h2><div id="oc_div_i14" class="oc_div lev2 hide"><p class="bld">Thousand views of thousand structures</p><a href="quick.php" target="_blank"><img src="../emnavi/img/about_ym.jpg" class="docimg" decoding="async"></a><p>URL: <a href="quick.php" target="_blank">https://pdbj.org/emnavi/quick.php</a></p><ul class="doc_ul"><li>Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.</li><li>This page is also the successor to <b>EM Navigator detail page</b>, and also detail information page/front-end page for <i>Omokage search</i>.</li><li>The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.</li></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=emdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=pdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">PDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=sasbdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">SASBDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=3databanks&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Comparison of 3 databanks</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ysearch&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Search</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=emn_repl&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Aug 31, 2016. New EM Navigator & Yorodumi</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_pap&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Papers</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=jmol&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Jmol/JSmol</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=func_homology&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Function and homology information</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=new_emn_changes&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Changes in new EM Navigator and Yorodumi</span></p></div><h2 id="h_i15" onclick="_hdiv.oc('i15')"><div id="oc_btn_i15" class="oc_btn">+</div>Yorodumi Search</h2><div id="oc_div_i15" class="oc_div lev2 hide"><p class="bld">Cross-search of EMDB, PDB, SASBDB, etc.</p><a href="ysearch.php" target="_blank"><img src="../emnavi/img/about_ysearch.jpg" class="docimg" decoding="async"></a><p>URL: <a href="ysearch.php" target="_blank">https://pdbj.org/emnavi/ysearch.php</a></p><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=emdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=pdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">PDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=sasbdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">SASBDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=3databanks&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Comparison of 3 databanks</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_esearch&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMN Search</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ym&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=met_data&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Experimental methods, equipments, and software data</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=func_homology&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Function and homology information</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=new_emn_changes&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Changes in new EM Navigator and Yorodumi</span></p></div><h2 id="h_i16" onclick="_hdiv.oc('i16')"><div id="oc_btn_i16" class="oc_btn">+</div>Yorodumi Papers</h2><div id="oc_div_i16" class="oc_div lev2 hide"><p class="bld">Database of articles cited by EMDB/PDB/SASBDB data</p><a href="pap.php" target="_blank"><img src="../emnavi/img/about_pap.jpg" class="docimg" decoding="async"></a><p>URL: <a href="pap.php" target="_blank">https://pdbj.org/emnavi/pap.php</a></p><ul class="doc_ul"><li>Database of articles cited by EMDB, PDB, and SASBDB entries</li><li>Using PubMed data</li></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=emdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=pdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">PDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=sasbdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">SASBDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ym&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_empap&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMN Papers</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=new_emn_changes&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Changes in new EM Navigator and Yorodumi</span></p></div><h2 id="h_i17" onclick="_hdiv.oc('i17')"><div id="oc_btn_i17" class="oc_btn">+</div>Yorodumi Speices</h2><div id="oc_div_i17" class="oc_div lev2 hide"><p class="bld">Taxonomy data in EMDB/PDB/SASBDB</p><a href="taxo.php" target="_blank"><img src="../emnavi/img/about_taxo.jpg" class="docimg" decoding="async"></a><p>URL: <a href="taxo.php" target="_blank">https://pdbj.org/emnavi/taxo.php</a></p><p>Taxonomy database of sample sources of data in EMDB/PDB/SASBDB</p><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=emdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=pdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">PDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=sasbdb&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">SASBDB</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=3databanks&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Comparison of 3 databanks</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=sars-cov-2&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Mar 5, 2020. Novel coronavirus structure data</span></p></div><h2 id="h_i18" onclick="_hdiv.oc('i18')"><div id="oc_btn_i18" class="oc_btn">+</div>Yorodumi Docs</h2><div id="oc_div_i18" class="oc_div lev2 hide"><p class="bld">Documentation for Yorodumi, EM Navigator, Omokage, etc.</p><a href="doc.php" target="_blank"><img src="../emnavi/img/about_doc.jpg" class="docimg" decoding="async"></a><p>URL: <a href="doc.php" target="_blank">https://pdbj.org/emnavi/doc.php</a></p></div><h2 id="h_i19" onclick="_hdiv.oc('i19')"><div id="oc_btn_i19" class="oc_btn">+</div>Covid-19 info</h2><div id="oc_div_i19" class="oc_div lev2 hide"><p class="bld">Page for Covid-19 featured contents</p><a href="covid19.php" target="_blank"><img src="../emnavi/img/about_covid19.jpg" class="docimg" decoding="async"></a><p>URL: <a href="covid19.php" target="_blank">https://pdbj.org/emnavi/covid19.php</a></p><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=3databanks&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Comparison of 3 databanks</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=newpage_covid19&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Aug 12, 2020. Covid-19 info</span></p></div><h2 id="h_i20" onclick="_hdiv.oc('i20')"><div id="oc_btn_i20" class="oc_btn">+</div>F&H Search</h2><div id="oc_div_i20" class="oc_div lev2 hide"><p class="bld">Function & Homology similarity search</p><a href="fh-search.php" target="_blank"><img src="../emnavi/img/about_fh_search.jpg" class="docimg" decoding="async"></a><p>URL: <a href="fh-search.php" target="_blank">https://pdbj.org/emnavi/fh-search.php</a></p><p>Based on the similarity of Function & Homolog items related to the structure data, similar data are searched from structure databases.</p><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=func_homology&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Function and homology information</span></p></div><h2 id="h_i21" onclick="_hdiv.oc('i21')"><div id="oc_btn_i21" class="oc_btn">+</div>Jmol/JSmol</h2><div id="oc_div_i21" class="oc_div lev2 hide"><p class="bld">An open-source viewer for chemical structures in 3D</p><ul class="doc_ul"><li>Mouse/touch operation<table><tr class="toprow"><th><th>X-Y rotation<th>X-Y move<th>Zoom in/out<tr><th>Mouse<td>left drag<td>[Ctrl] + right drag<td>center drag (vertical) / wheel<tr><th>Touch<td>single finger<td>double finger<td>pinch</table></li><li>Jmol menu: [Ctrl] + click / right click</li></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=molmil&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Molmil</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ym&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi</span></p><p class="small"><b>External links</b>:<a href="https://jmol.sourceforge.net/" target="_blank"><img src="img/lk-link.gif" class="lkicon">Jmol: an open-source Java viewer for chemical structures in 3D</a></p></div><h2 id="h_i22" onclick="_hdiv.oc('i22')"><div id="oc_btn_i22" class="oc_btn">+</div>Molmil</h2><div id="oc_div_i22" class="oc_div lev2 hide"><p class="bld">WebGL based molecular viewer</p><ul class="doc_ul"><li>Molmil runs on Web browser on a smartphone or tablet device as well as PC. (Molmil is based on WebGL and Javascript).</li><li>Mouse/touch operation<table><tr class="toprow"><th><th>X-Y rotation<th>X-Y move<th>Zoom in/out<tr><th>Mouse<td>left drag<td>center drag / shift + left drag<td>right drag / wheel<tr><th>Touch<td>single finger<td>double finger<td>pinch</table></li><li>Function menu: top left buttons on viewer screen</li></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=jmol&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Jmol/JSmol</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=surfview&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">SurfView</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=new_emn_changes&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Changes in new EM Navigator and Yorodumi</span></p><p class="small"><b>External links</b>:<a href="https://pdbj.org/help/molmil" target="_blank"><img src="img/lk-link.gif" class="lkicon">Documentation of Molmil in PDBj site</a><span class="sep"> / </span><a href="https://github.com/gjbekker/molmil" target="_blank"><img src="img/lk-link.gif" class="lkicon">Molmil page in GitHub</a></p></div><h2 id="h_i23" onclick="_hdiv.oc('i23')"><div id="oc_btn_i23" class="oc_btn">+</div>Carbohydrate representation</h2><div id="oc_div_i23" class="oc_div lev2 hide"><p class="bld">Polysaccaride/carbohydrate data representation in PDB</p><ul class="doc_ul"><li>In July 2020, representation for polysaccaride/carbohydrate information in PDB is improved.</li><li>The polysaccaride figures are generated by GlycanBuilder2.</li><li>See following external links for details.</li></ul><p class="small"><b>External links</b>:<a href="https://www.sciencedirect.com/science/article/pii/S0008621516305316" target="_blank"><img src="img/lk-link.gif" class="lkicon">Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans - ScienceDirect</a><span class="sep"> / </span><a href="http://www.rings.t.soka.ac.jp/downloads.html" target="_blank"><img src="img/lk-link.gif" class="lkicon">GlycanBuilder2 - RINGS (Resource For INformatics Of Glycomes at Soka)</a><span class="sep"> / </span><a href="https://www.wwpdb.org/documentation/carbohydrate-remediation" target="_blank"><img src="img/lk-link.gif" class="lkicon">Carbohydrate Remediation - wwPDB documentation</a><span class="sep"> / </span><a href="https://www.wwpdb.org/news/news?year=2020#5f0495919902836395e11ce8" target="_blank"><img src="img/lk-link.gif" class="lkicon">Coming July 29: Improved Carbohydrate Data at the PDB - wwPDB news</a></p></div><h2 id="h_i24" onclick="_hdiv.oc('i24')"><div id="oc_btn_i24" class="oc_btn">+</div>Experimental methods, equipments, and software data</h2><div id="oc_div_i24" class="oc_div lev2 hide"><p class="bld">Database of experimental methods of EMDB, PDB and SABDB.</p><p>URL: <a href="ysearch.php?&act_tab=met" target="_blank">https://pdbj.org/emnavi/ysearch.php?&act_tab=met</a></p><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=3databanks&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Comparison of 3 databanks</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ysearch&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Search</span></p></div><h2 id="h_i25" onclick="_hdiv.oc('i25')"><div id="oc_btn_i25" class="oc_btn">+</div>Function and homology information</h2><div id="oc_div_i25" class="oc_div lev2 hide"><p class="bld">Molecular function, domain, and homology information from related databases.</p><ul class="doc_ul"><li>To help to understand the molecular function and to find the related structure data, Yorodumi and Yorodumi Search display and utilize the related database information about function and homology.</li><li>In addition to the information of EC, EMBL, GeneBank, GO, InterPro, UniProt, etc. stored in the EMDB header XML, PDBx/mmCIF and sasCIF original data, information of Pfam, PROSITE, Reactome, UniProkKB, etc. are collected via PDBMLplus, EMDB-PDB fitting data, and/or UniProt.<table><tr class="toprow"><th>Category<th>Name of database or definition<tr><th>Function%<td>Gene ontology, Enzyme Commission number, Reactome, etc.<tr><th>Domain/homology<td>CATH, InterPro, SMART, etc.<tr><th>Component<td>UniProt, GenBank, PDB chemical component, etc.</table></li></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_fh_search&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">F&H Search</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=mlplus&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Information from PDBMLplus</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ysearch&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Search</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ym&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_fh_search&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">F&H Search</span></p></div><h2 id="h_i26" onclick="_hdiv.oc('i26')"><div id="oc_btn_i26" class="oc_btn">+</div>Changes in new EM Navigator and Yorodumi</h2><div id="oc_div_i26" class="oc_div lev2 hide"><p class="bld">Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)</p><ul class="doc_ul"><li>Changes:</li><ul class="doc_ul"><li>New user interface unified in <i>EM Navigator</i>, <i>Yorodumi</i> & <i>Omokage search</i>, supporting mobile devices as well as PCs.</li><li>New <i>Yorodumi</i> replace the individual data page (<i>"Detail page"</i> of EM Navigator in the legacy system). It is unified browser for EMDB, PDB, and SASBDB entries integrated with <i>EM Navigator</i> and <i>Omokage search</i>.</li><li>The viewers (structure/movie viewers) appear in pop-up windows. On a PC, multiple viewer windows can be opened. On mobile devices, the viewers support touch operation.</li></ul><li>New features:</li><ul class="doc_ul"><li><b><i>Molmil</i></b>, molecular structure viewer, and <b><i>SurfView</i></b>, surface model viewer for EMDB map data, are available to view the 3D structures. Both viewers support mobile device use.</li><li>Yorodumi support SASBDB entries.</li><li>Some new pages such as <b><i>Yorodumi Papers</i></b>, citation database of structure data entries and <b><i>Yorodumi Search</i></b>, cross search by keywords</li></ul></ul><p class="small"><b>Related info.</b>:<span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_emn&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EM Navigator</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ym&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=surfview&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">SurfView</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=molmil&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Molmil</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=movie&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Movie viewer</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_empap&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">EMN Papers</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_pap&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Papers</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=about_ysearch&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Search</span><span class="sep"> / </span><span onclick="_pop.up(this)" data-pop="<span class="loadingbar"><img src="img/loading.gif" decoding="async"></span>" data-url="ajax.php?mode=doc&id=emn_repl&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Aug 31, 2016. New EM Navigator & Yorodumi</span></p></div><h2 id="h_i27" onclick="_hdiv.oc('i27')"><div id="oc_btn_i27" class="oc_btn">+</div>Information from PDBMLplus</h2><div id="oc_div_i27" class="oc_div lev2 hide"><p class="bld">PDBMLplus is the XML format file including additional information relating to individual proteins. Currently, PDB files are lacking a detailed description of function, experimental conditions, and the like. 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Suzuki</a></div></footer></div><div id="popbox" class="popbox"></div><div id="popbox2" class="popbox"></div><div id="popbox3" class="popbox"></div><datalist id="acomp_kw"><option value="FEI"><option value="KRIOS"><option value="TITAN"><option value="VITROBOT"><option value="MARK"><option value="RELION"><option value="SUPPRESSED"><option value="COMPLEX"><option value="TECNAI"><option value="WITH"><option value="FAB"><option value="CRYOSPARC"><option value="ARCTICA"><option value="TALOS"><option value="HUMAN"><option value="SPIRIT"><option value="VIRUS"><option value="THE"><option value="SERUM"><option value="POLARA"><option value="POLYCLONAL"><option value="BG50"><option value="III"><option value="F20"><option value="RM19N"><option value="FROM"><option value="PLUNGER"><option value="STRUCTURE"><option value="HOMEMADE"><option value="AND"><option value="LEICA"><option value="CISTEM"><option value="CARDIAC"><option value="IMOD"><option value="BOUND"><option value="THIN"><option value="MOTOR"><option value="OTHER"><option value="F30"><option value="JEOL"><option value="CORE"><option value="CHANNEL"><option value="MAP"><option value="NUCLEOSOME"><option value="TRIC"><option value="BOMBYX"><option value="MORI"><option value="LOCAL"><option value="ADENO-ASSOCIATED"><option value="ETOMO"><option value="70S"><option value="FLAGELLAR"><option value="MICROTUBULE"><option value="RECEPTOR"><option value="CYPOVIRUS"><option value="NATIVE"><option value="AFRICAN"><option value="STRAIN"><option value="COLI"><option value="GAMMA-TUBULIN"></datalist><script> var phpvar={"loading":"<p><span class=\"loadingbar\"><img src=\"img\/loading.gif\" decoding=\"async\"><\/span>Loading...<\/p>","loadingerror":"<span class=\"red\"> error?<\/span>","vwurl":{"molmil":"pop_molmil.php?id=","jmol":"pop_jmol.php?id=","mov":"pop_mov.php?id=","sview":"pop_sview.php?id="},"movidx_bar":"<li class=\"clearfix hide\"><button class=\"closebtn\" onclick=\"_pmov.win(0,this)\">X<\/button><span onclick=\"_pmov.win(1,this)\"><img src=\"data\/__imgurl__\" class=\"extcol_listitem_img\" decoding=\"async\">__str__<\/span><\/li>","vwidx_bar":"<li class=\"clearfix hide\"><button class=\"closebtn\" onclick=\"_vw.win(0,this)\">X<\/button><span onclick=\"_vw.win(1,this)\"><img src=\"data\/__imgurl__\" class=\"extcol_listitem_img\" decoding=\"async\">__str__<\/span><\/li>","imgurl":{"mov":{"e":"emdb\/media\/__id__\/snapss__num__.jpg","p":"pdb\/media\/__id__\/snapss__num__.jpg"},"vw":{"e":"emdb\/media\/__id__\/snapss2.jpg","p":"pdb\/img\/__id__.jpg","s":"sas\/img\/__id__.jpg","c":"chem\/img\/__id__.gif","b":"bird\/img\/__id__.gif"}},"idservadr":"ajax.php?mode=id2img&id=","popxbtn":{"1":"<button onclick=\"_pop.hide()\" class=\"pophide\">X<\/button>","2":"<button onclick=\"_pop.hide(2)\" class=\"pophide\">X<\/button>","3":"<button onclick=\"_pop.hide(3)\" class=\"pophide\">X<\/button>"}};jQuery.fn.extend({_loadex:function(opt){var $cont_box=$(this);var speed=opt.speed===undefined?"medium":opt.speed;var $body=$("html,body");_pop.hide();if($cont_box.offset().top<$body.scrollTop())$("html,body").stop(1,1).animate({scrollTop:$cont_box.offset().top},"slow");return $cont_box.slideUp(speed,function(){$cont_box.html(phpvar.loading).show().load(opt.u,opt.v,opt.func)})}}); 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function _entitem(type,data_id,movnum){var id=data_id.replace(/^.+-/,"");var db=data_id.substr(0,1).toLowerCase();return type=="mol"?phpvar.vwidx_bar.replace("__imgurl__",phpvar.imgurl.vw[db].replace("__id__",id)).replace("__str__",id):phpvar.movidx_bar.replace("__imgurl__",phpvar.imgurl.mov[db].replace("__id__",id).replace("__num__",movnum||(db=="e"?2:"dep"))).replace("__str__",id+(movnum?" #"+movnum:""))}; </script>

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