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Shape similarity search of macromolecules - Omokage search
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class="clickable" onclick="_hdiv.focus('query')">Search query</li><li class="clickable" onclick="_hdiv.focus('about')"><img src="img/lk-help.gif" class="lkicon">About Omokage search</li></ul></div><h2 id="h_i20" onclick="_hdiv.oc('i20')"><div id="oc_btn_i20" class="oc_btn">-</div>This web site</h2><div id="oc_div_i20" 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-omokage.gif" decoding="async"><span itemprop="title">Omokage search</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_i21" onclick="_hdiv.oc('i21')"><div id="oc_btn_i21" class="oc_btn">-</div><img src="img/lk-opt.gif" class="lkicon">Options</h2><div id="oc_div_i21" class="oc_div lev2"><ul><li><b>[English]</b> <a href="/emnavi/omo-search.php?lang=ja">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/omo-search.php?lang=ja">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-omokage.gif" decoding="async"><span itemprop="title">Omokage search</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; 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class="ttcol1">Omo</span><span class="ttcol2">kage</span> search</span><div id="simple_top_sub">- Shape similarity search of macromolecules -</div></div></header><div id="maininner"><h1 id="h_query" onclick="_hdiv.oc('query',2)"><div id="oc_btn_query" class="oc_btn">-</div>Search query</h1><div id="oc_div_query" class="oc_div lev1"><div><p class="tabp"><span class="tabstr">Query structure data: </span><span class="wrap hide"><br></span><button id="tabbtn_i9_i10" type="button" class="tabbtn tabbtn_i9" disabled onclick="_tab.s('i9','i10')" autocomplete="off"><i class="fa fa-database dark large"></i><b>Registered data</b><br>structure in databanks</button><button id="tabbtn_i9_i11" type="button" class="tabbtn tabbtn_i9" onclick="_tab.s('i9','i11')" autocomplete="off"><i class="fa fa-upload dark large"></i><b>Upload</b><br>your original/modified data</button></p><div id="tabdiv_i9_i10" class="tabdiv tabdiv_i9">ID of EMDB, PDB or SASBDB: <form id="id_form" method="get"><input type="search" name="id" id="idbox" size="15" class="acomp" list="acomp_omoid"><input type="hidden" name="img_mode" value="ym"><input type="submit" class="submitbtn" value="Search"></form><button onclick="_more('i1')" id="moreb_i1">?</button><button onclick="_more('i1',1)" id="lessb_i1" class="hide">hide</button><div id="more_i1" class="hide"><ul><li><b>EMDB map</b><ul><li>4 or 5 digit ID<li>or string starts with "e"<li><span green><i>e.g.</i> 1003, EMD-1003, e1003</span></ul><li><b>PDB deposited unit (asymetric unit, AU) </b><ul><li>4 letter ID code<li>or ID code + hyphen + "d"<li><span green><i>e.g.</i> 100d, 100d-d</span></ul><li><b>PDB assembly (biological unit, BU)</b><ul><li>ID + hyphen + assembly-ID<li>Or click the image of AU/BU, which will be shown below when you input an PDB-ID<li><span green><i>e.g.</i> 1oel-1</span></ul><li><b>SASBDB model</b><ul><li>SASBDB-ID<li>or SASBDB-model-ID<li><span green><i>e.g.</i> SASDAA5, 100, sas-100</span></ul></ul><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></div><div id="ent_info"></div><div class="clboth"></div><div><p class="tabp"><span class="tabstr">Samples: </span><span class="wrap hide"><br></span><button id="tabbtn_sampleids_i2" type="button" class="tabbtn tabbtn_sampleids" disabled onclick="_tab.s('sampleids','i2')" autocomplete="off">Recommended</button><button id="tabbtn_sampleids_i3" type="button" class="tabbtn tabbtn_sampleids" onclick="_tab.s('sampleids','i3')" autocomplete="off">EMDB</button><button id="tabbtn_sampleids_i4" type="button" class="tabbtn tabbtn_sampleids" onclick="_tab.s('sampleids','i4')" autocomplete="off">PDB</button><button id="tabbtn_sampleids_i5" type="button" class="tabbtn tabbtn_sampleids" onclick="_tab.s('sampleids','i5')" autocomplete="off">SASBDB</button></p><div id="tabdiv_sampleids_i2" class="tabdiv tabdiv_sampleids">Structure data giving symbolic results <button onclick="$('.sampledesc').toggle(200);">Show details</button><br><img src="data/emdb/media/2190/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e2190',this);" decoding="async"><p class="clearfix sampledesc">This is an EM map data of the RNA polymerase II at 25 A resolution. You will find atomic models and EM maps of RNA polymerase structures from the EMDB & PDB.<a href="?id=e2190">_Perform search.</a></p><img src="data/pdb/img_dep/3ifv.jpg" class="enticon sampleicon" onclick="_sample('3ifv-d',this);" decoding="async"><p class="clearfix sampledesc">The DNA clamp is a ring shaped oligomer essential for DNA metabolism. All the DNA clamps have similar shapes, while bacterial clamps are dimer ring, and archaeal/eukaryal ones are trimer ring. By search using this trimer clamp, you will find dimer clamp structures as well.<a href="?id=3ifv-d">_Perform search.</a></p><img src="data/pdb/img_dep/1ob2.jpg" class="enticon sampleicon" onclick="_sample('1ob2-d',this);" decoding="async"><p class="clearfix sampledesc">EF-Tu/tRNA complex (RNA + protein) and EF-G (monomeric protein) have similar shapes despite their different compositions ("molecular mimicry"). You will find both EFs by this search.<a href="?id=1ob2-d">_Perform search.</a></p><img src="data/sas/img/135.jpg" class="enticon sampleicon" onclick="_sample('s135',this);" decoding="async"><p class="clearfix sampledesc">This is a dummy-atom model of lumazine synthase obtained by SAS. You will find many crystal structures and EM maps of same molecules.<a href="?id=s135">_Perform search.</a></p><img src="data/emdb/media/1003/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e1003',this);" decoding="async"><p class="clearfix sampledesc">Many 70S ribosome structure data are stored in EMDB and PDB. Omokage search is useful to find out such the huge molecule structures.<a href="?id=e1003">_Perform search.</a></p><img src="data/pdb/img_asb/1uf2_1.jpg" class="enticon sampleicon" onclick="_sample('1uf2-1',this);" decoding="async"><p class="clearfix sampledesc">For huger molecule, such as this rice dwarf virus, Omokage search can be used.<a href="?id=1uf2-1">_Perform search.</a></p><img src="data/pdb/img_dep/1dl4.jpg" class="enticon sampleicon" onclick="_sample('1dl4-d',this);" decoding="async"><p class="clearfix sampledesc">Not only for the huge structures but also for small molecules, such as this DNA fragment, this tool might be useful. By this search, some proteins having similar shape to this DNA fragment are found (for good or for bad).<a href="?id=1dl4-d">_Perform search.</a></p><img src="data/pdb/img_dep/4es0.jpg" class="enticon sampleicon" onclick="_sample('4es0-d',this);" decoding="async"><p class="clearfix sampledesc">This is another example for small molecules. Which proteins have simialar shapes to this beta-propeller structure?<a href="?id=4es0-d">_Perform search.</a></p></div><div id="tabdiv_sampleids_i3" class="tabdiv tabdiv_sampleids hide"><p><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></p><img src="data/emdb/media/1022/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e1022',this);" decoding="async"><img src="data/emdb/media/1531/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e1531',this);" decoding="async"><img src="data/emdb/media/1603/mapi/surf_z.jpg" class="enticon sampleicon" onclick="_sample('e1603',this);" decoding="async"><img src="data/emdb/media/1714/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e1714',this);" decoding="async"><img src="data/emdb/media/2651/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e2651',this);" decoding="async"><img src="data/emdb/media/5001/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e5001',this);" decoding="async"><img src="data/emdb/media/5130/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e5130',this);" decoding="async"><img src="data/emdb/media/5225/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e5225',this);" decoding="async"><img src="data/emdb/media/5438/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e5438',this);" decoding="async"><img src="data/emdb/media/5646/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e5646',this);" decoding="async"><img src="data/emdb/media/6106/snaps2.jpg" class="enticon sampleicon" onclick="_sample('e6106',this);" decoding="async"></div><div id="tabdiv_sampleids_i4" class="tabdiv tabdiv_sampleids hide"><p><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></p><img src="data/pdb/img_dep/1a00.jpg" class="enticon sampleicon" onclick="_sample('1a00-d',this);" decoding="async"><img src="data/pdb/img_asb/1cg6_1.jpg" class="enticon sampleicon" onclick="_sample('1cg6-1',this);" decoding="async"><img src="data/pdb/img_dep/1g8w.jpg" class="enticon sampleicon" onclick="_sample('1g8w-d',this);" decoding="async"><img src="data/pdb/img_dep/1hen.jpg" class="enticon sampleicon" onclick="_sample('1hen-d',this);" decoding="async"><img src="data/pdb/img_asb/1opf_1.jpg" class="enticon sampleicon" onclick="_sample('1opf-1',this);" decoding="async"><img src="data/pdb/img_dep/1ryp.jpg" class="enticon sampleicon" onclick="_sample('1ryp-d',this);" decoding="async"><img src="data/pdb/img_asb/1xi5_1.jpg" class="enticon sampleicon" onclick="_sample('1xi5-1',this);" decoding="async"><img src="data/pdb/img_dep/2qc9.jpg" class="enticon sampleicon" onclick="_sample('2qc9-d',this);" decoding="async"><img src="data/pdb/img_asb/2r4p_1.jpg" class="enticon sampleicon" onclick="_sample('2r4p-1',this);" decoding="async"><img src="data/pdb/img_dep/2rcs.jpg" class="enticon sampleicon" onclick="_sample('2rcs-d',this);" decoding="async"><img src="data/pdb/img_asb/2xct_1.jpg" class="enticon sampleicon" onclick="_sample('2xct-1',this);" decoding="async"><img src="data/pdb/img_asb/3ajp_1.jpg" class="enticon sampleicon" onclick="_sample('3ajp-1',this);" decoding="async"><img src="data/pdb/img_dep/3bri.jpg" class="enticon sampleicon" onclick="_sample('3bri-d',this);" decoding="async"><img src="data/pdb/img_dep/3cre.jpg" class="enticon sampleicon" onclick="_sample('3cre-d',this);" decoding="async"><img src="data/pdb/img_dep/3lz0.jpg" class="enticon sampleicon" onclick="_sample('3lz0-d',this);" decoding="async"><img src="data/pdb/img_asb/3p4g_3.jpg" class="enticon sampleicon" onclick="_sample('3p4g-3',this);" decoding="async"><img src="data/pdb/img_asb/3vmy_1.jpg" class="enticon sampleicon" onclick="_sample('3vmy-1',this);" decoding="async"><img src="data/pdb/img_asb/4bse_1.jpg" class="enticon sampleicon" onclick="_sample('4bse-1',this);" decoding="async"><img src="data/pdb/img_dep/4gxl.jpg" class="enticon sampleicon" onclick="_sample('4gxl-d',this);" decoding="async"><img src="data/pdb/img_dep/4hfh.jpg" class="enticon sampleicon" onclick="_sample('4hfh-d',this);" decoding="async"><img src="data/pdb/img_asb/4mya_1.jpg" class="enticon sampleicon" onclick="_sample('4mya-1',this);" decoding="async"><img src="data/pdb/img_asb/6r1r_4.jpg" class="enticon sampleicon" onclick="_sample('6r1r-4',this);" decoding="async"><img src="data/pdb/img_dep/6tna.jpg" class="enticon sampleicon" onclick="_sample('6tna-d',this);" decoding="async"><img src="data/pdb/img_asb/1k4c_1.jpg" class="enticon sampleicon" onclick="_sample('1k4c-1',this);" decoding="async"><img src="data/pdb/img_dep/4mna.jpg" class="enticon sampleicon" onclick="_sample('4mna-d',this);" decoding="async"></div><div id="tabdiv_sampleids_i5" class="tabdiv tabdiv_sampleids hide"><p><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></p><img src="data/sas/img/8.jpg" class="enticon sampleicon" onclick="_sample('s8',this);" decoding="async"><img src="data/sas/img/39.jpg" class="enticon sampleicon" onclick="_sample('s39',this);" decoding="async"><img src="data/sas/img/100.jpg" class="enticon sampleicon" onclick="_sample('s100',this);" decoding="async"><img src="data/sas/img/36.jpg" class="enticon sampleicon" onclick="_sample('s36',this);" decoding="async"><img src="data/sas/img/68.jpg" class="enticon sampleicon" onclick="_sample('s68',this);" decoding="async"><img src="data/sas/img/116.jpg" class="enticon sampleicon" onclick="_sample('s116',this);" decoding="async"><img src="data/sas/img/239.jpg" class="enticon sampleicon" onclick="_sample('s239',this);" decoding="async"></div></div></div><div id="tabdiv_i9_i11" class="tabdiv tabdiv_i9 hide">You can use your original data or a modified data for the search. Select type of the file and upload the file by this form.<div><p class="tabp"><span class="tabstr">Data type: </span><span class="wrap hide"><br></span><button id="tabbtn_data_type_i6" type="button" class="tabbtn tabbtn_data_type" disabled onclick="_tab.s('data_type','i6')" autocomplete="off">Model</button><button id="tabbtn_data_type_i7" type="button" class="tabbtn tabbtn_data_type" onclick="_tab.s('data_type','i7')" autocomplete="off">Density map</button><button id="tabbtn_data_type_i8" type="button" class="tabbtn tabbtn_data_type" onclick="_tab.s('data_type','i8')" autocomplete="off">Codebook vectors</button></p><div id="tabdiv_data_type_i6" class="tabdiv tabdiv_data_type"><ul><li>This is a search using PDB format coordinate file (atomic model, SAXS bead model, etc)<li>Uncompressed or gzip-compressed file can be used</ul><form method="post" enctype="multipart/form-data"><table><tr><th>File<td><input type="file" required name="pdb"></table><input type="submit" style="width:20em" class="submitbtn"></form></div><div id="tabdiv_data_type_i7" class="tabdiv tabdiv_data_type hide"><ul><li>This is a search using 3D density map file in CCP4/MRC format.<li>Only for map with cubic voxels.<li>Max voxel number is ~200. Large map data should be trimmed and shrined before uploading.<li>Uncompressed or gzip-compressed file can be used</ul><form method="post" enctype="multipart/form-data"><table><tr><th>File<td><input type="file" required name="map"><tr><th>Surface level<td><input type="number" name="thr" size="10" step="any" value="1"></table><input type="submit" style="width:20em" class="submitbtn"></form></div><div id="tabdiv_data_type_i8" class="tabdiv tabdiv_data_type hide"><ul><li>This is a search using "Codebook" vectors made by <i>qvol</i> or <i>qpdb</i> tool in <a href="http://situs.biomachina.org" target="_blank"><i>Situs</i> package</a>. Two models, model with 30 and 50 points are required for Omokage comparison. " ,</ul><form method="post" enctype="multipart/form-data"><table><tr><th>30-dot model<td><input type="file" required name="vq30"><tr><th>50-dot model<td><input type="file" required name="vq50"></table><input type="submit" style="width:20em" class="submitbtn"></form></div></div></div></div><datalist id="acomp_omoid"></datalist></div><div id="subj_box"></div><div id="result_box" class="clboth"></div><h1 id="h_about" onclick="_hdiv.oc('about')"><div id="oc_btn_about" class="oc_btn">-</div><img src="img/lk-help.gif" class="lkicon">About Omokage search</h1><div id="oc_div_about" class="oc_div lev1"><h2 id="h_i17" onclick="_hdiv.oc('i17')"><div id="oc_btn_i17" class="oc_btn">-</div>News</h2><div id="oc_div_i17" class="oc_div lev2"><h3 id="h_i12" onclick="_hdiv.oc('i12')"><div id="oc_btn_i12" class="oc_btn">-</div>Aug 12, 2020. Covid-19 info</h3><div id="oc_div_i12" class="oc_div"><p class="bld">Covid-19 info</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>New page: Covid-19 featured information page in EM Navigator.</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=about_covid19&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Covid-19 info</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><h3 id="h_i13" onclick="_hdiv.oc('i13')"><div id="oc_btn_i13" class="oc_btn">-</div>Mar 5, 2020. Novel coronavirus structure data</h3><div id="oc_div_i13" class="oc_div"><p class="bld">Novel coronavirus structure data</p><ul class="doc_ul"><li>International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".</li><ul class="doc_ul"><li><a href="https://www.nature.com/articles/s41564-020-0695-z" target="_blank">The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology</a></li></ul><li>In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.</li><ul class="doc_ul"><li><a href="taxo.php?k=2697049" target="_blank">Severe acute respiratory syndrome coronavirus 2 | Severe acute respiratory syndrome coronavirus 2</a></li><li><a href="ysearch.php?kw=SARS-CoV-2" target="_blank">SARS-CoV-2 - Yorodumi Search</a></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_taxo&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Yorodumi Speices</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><p class="small"><b>External links</b>:<a href="https://pdbj.org/featured/covid-19" target="_blank"><img src="img/lk-link.gif" class="lkicon">COVID-19 featured content - PDBj</a><span class="sep"> / </span><a href="https://numon.pdbj.org/mom/242" target="_blank"><img src="img/lk-link.gif" class="lkicon">Molecule of the Month (242)：Coronavirus Proteases</a></p></div><h3 id="h_i14" onclick="_hdiv.oc('i14')"><div id="oc_btn_i14" class="oc_btn">+</div>Jul 12, 2017. Major update of PDB</h3><div id="oc_div_i14" class="oc_div hide"><p class="bld">Major update of PDB</p><ul class="doc_ul"><li>wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.</li><li>This is a major update changing the version number from 4 to 5, and with <i>Remediation</i>, in which all the entries are updated.</li><li>In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).</li><li>Now, EM Navigator and Yorodumi are based on the updated data.</li></ul><p class="small"><b>External links</b>:<a href="https://www.wwpdb.org/documentation/remediation" target="_blank"><img src="img/lk-link.gif" class="lkicon">wwPDB Remediation</a><span class="sep"> / </span><a href="https://www.wwpdb.org/news/news?year=2017#5963997661fd3d50915a4af7" target="_blank"><img src="img/lk-link.gif" class="lkicon">Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive</a></p></div><h3 id="h_i15" onclick="_hdiv.oc('i15')"><div id="oc_btn_i15" class="oc_btn">+</div>Jun 16, 2017. Omokage search with filter</h3><div id="oc_div_i15" class="oc_div hide"><p class="bld">Omokage search with filter</p><p>Result of Omokage search can be filtered by keywords and the database types</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=about_omosearch&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Omokage search</span></p></div><h3 id="h_i16" onclick="_hdiv.oc('i16')"><div id="oc_btn_i16" class="oc_btn">+</div>Apr 13, 2016. 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By comparing <b>global shapes</b>, and ignoring details, similar-shaped structures are searched.</li><li>The search is performed ageinst >200,000 structure data, which consists of EMDB map data, PDB coordinates (deposited units (asymmetric units, usually), PDB biological units, and SASBDB mdoels).</li><li>For the search query, you can use either a data in the PDB/EMDB/SASBDB or your original model.</li><li>Supported formats are PDB (atomic model, SAXS bead model, etc.) and CCP4/MRC map (3D density map).</li><li>Shape comparison is performed by iDR profile method, which uses 1D-distance profiles of super-simplified models generated by vector quantizaion in <i>Situs</i> package.</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=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=5&ajax=1" class="poptrg"><img src="img/lk-help.gif" class="lkicon">Sep 22, 2014. 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o.focus()})},close:function(){$("#movlist").html("");this.$menuctrl.slideUp("fast");this.all(function(o){o.close()})},tile:function(){var x=y=y_nex=x_win=y_win=0,x_scr=window.parent.screen.width,y_scr=window.parent.screen.height,mgn=2;$.each(this.wins,function(win_id,o){x_win=o.outerWidth;y_win=o.outerHeight;if(x+x_win>x_scr){x=0;y=y_nex}o.moveTo(x,y);y_nex=y_nex>y+y_win?y_nex:y+y_win;x=o.screenX+x_win+mgn;if(y>y_scr)y=0;o.focus()})},all:function(fn){$.each(this.wins,function(win_id,o_win){if(o_win.closed)this.closed(win_id); else fn(o_win)}.bind(this))},win:function(flg,domobj){var wid=$(domobj).parent().data("wid");var o=this.wins[wid];if(!o||o.closed)this.closed(wid);flg?o.focus():o.close()},closed:function(win_id){delete this.wins[win_id];$("#movidx_"+win_id).hide("medium",function(){$(this).detach()});if(Object.keys(this.wins).length==0)this.$menuctrl.slideUp("fast")}}; _vw={wins:{},cmdhist_lastid:false,cmdhist_lastmsg:false,qtimer:{},qloopcnt:{},ques:{},conf:{apps:{mol:_localstr.get("viewer.apps.mol")||"molmil",map:_localstr.get("viewer.apps.map")||"sview"},winsize:_localstr.getjson("viewer.winsize")||[500,500]},$menu_apps:{map:$(".menu_viewer_map"),mol:$(".menu_viewer_mol")},$menuctrl:$("#vwctrl"),$cmdhist_box:$("#cmdhist"),$pick_id:$("#p_id"),$pick_chain:$("#p_chain"),$pick_res:$("#p_res"),$pick_atom:$("#p_atom"),$pick_img:$("#p_img"),init_vwmenu:function(){this.$menu_apps.map.val(this.conf.apps.map); this.$menu_apps.mol.val(this.conf.apps.mol)},select_defvw:function(type,domobj){var v=$(domobj).val();if(v==this.conf.apps[type])return;this.conf.apps[type]=v;_localstr.set("viewer.apps."+type,v);this.init_vwmenu()},open:function(did,param){var o={};var viewer_appli=this.conf.apps[param&¶m.map?"map":"mol"];var win_id=viewer_appli+"-"+did;this.$menuctrl.slideDown("fast");if(param){if(param.obj)o=$(param.obj).data(viewer_appli);if(param.cmd&¶m.cmd[viewer_appli])o=param.cmd[viewer_appli];if(o){o.trg_obj= param.obj;this.que(win_id,o,viewer_appli)}}if(this.wins[win_id]&&!this.wins[win_id].closed){this.wins[win_id].focus();return false}$(_entitem("mol",did)).appendTo("#vwlist").attr("id","vwidx_"+win_id).data("wid",win_id).slideDown("medium");this.wins[win_id]=window.open(phpvar.vwurl[viewer_appli]+did,win_id,"menubar=no,location=no,scrollbars=0,"+"width="+this.conf.winsize[0]+",height="+this.conf.winsize[1]);return true},que:function(win_id,que,vapp){if(!que)return;vapp=vapp||"viewer";this.ques[win_id]= this.ques[win_id]||[];this.ques[win_id].push(que);clearInterval(this.qtimer[win_id]);this.qloopcnt[win_id]=0;this.qtimer[win_id]=setInterval(function(){++this.qloopcnt[win_id];if(this.qloopcnt[win_id]>50){this.msg_que(win_id,"timeout");this.clear_que(win_id);return}if(this.wins[win_id]&&this.wins[win_id].closed){this.clear_que(win_id);delete this.wins[win_id];this.msg_que(win_id,"window is closed");return}if(!this.wins[win_id]||!this.wins[win_id]._popvw||!this.wins[win_id]._popvw.ready){this.msg_que(win_id, "not ready");return}clearInterval(this.qtimer[win_id]);this.wins[win_id].focus();this.wins[win_id]._popvw.que_exe(this.ques[win_id]);this.clear_que(win_id);this.msg_que(win_id,"ok")}.bind(this),500)},clear_que:function(win_id){this.ques[win_id]=[];clearInterval(this.qtimer[win_id])},msg_que:function(win_id,str){this.cmdhist(win_id,"que of "+win_id+": "+str)},win:function(flg,domobj){var wid=$(domobj).parent().data("wid");var o=this.wins[wid];if(!o||o.closed)this.closed(wid);if(flg){window.blur(); o.focus()}else o.close()},winsized:function(wh){_localstr.setjson("viewer.winsize",wh);this.conf.winsize=[wh[0],wh[1]]},close_all:function(){$.each(this.wins,function(win_id,o_win){if(o_win.closed)return;o_win.close()});this.$menuctrl.slideUp("fast")},closed:function(win_id){delete this.wins[win_id];this.cmdhist(win_id,"Window closed","green");$("#vwidx_"+win_id).hide("medium",function(){$(this).detach()});if(Object.keys(this.wins).length==0){this.cmdhist("","All closed","green");this.$menuctrl.slideUp("fast")}}, cmdhist:function(win_id,str,col){if(!str)return;if(this.cmdhist_lastmsg==win_id+str)return;this.cmdhist_lastmsg=win_id+str;if(win_id!=this.cmdhist_lastid){this.$cmdhist_box.append('<p class="green bld">['+win_id+"]</p>");this.cmdhist_lastid=win_id}this.$cmdhist_box.append("<p></p>");this.$cmdhist_box.children("p:last").text(str).addClass(col);if(this.$cmdhist_box.children("p").length>100)this.$cmdhist_box.children("p:first").remove();this.$cmdhist_box.scrollTop(1E4)},mousepick:function(wn,str){var a= str.replace(/^.*?\[(.+?)\](.+?):(.+?)\.(.+?) #(.*?) .+$/,"$1,$2,$3,$4,$5").split(",");this.$pick_id.text(wn.replace("jmol-",""));this.$pick_chain.text(a[2]);this.$pick_res.text(a[0]+"-"+a[1]);this.$pick_atom.text(a[3]+"-"+a[4]);var o=this.$pick_img;$.get(phpvar.idservadr+a[0],function(data){if(data=="")o.slideUp("fast");else o.html(data).slideDown("fast")})}}; 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:""))}; var $subjbox=$("#subj_box"),$sicon=$(".sampleicon");phpvar.idservadr="omo-ajax.php?ent=1&id=";$(function(){if(phpvar.id){_result.start();_getsubj()}}); var _result={$box:$("#result_box"),$test:$("#test_box"),timer:null,start:function(){this.timer=setInterval(function(){this.get()}.bind(this),1E3);this.get()},get:function(){$.ajax({url:phpvar.ajaxurl,dataType:"json",data:phpvar.postvar,cache:false,success:function(json){if(json.end){_pop.hide();clearInterval(this.timer)}this.$box.html(json.out);this.$test.append(json.test).show()}.bind(this),error:function(jqXHR,textStatus,errorThrown){this.$test.show().html("<b>Error:</b> "+textStatus+"<br>"+"<b>Text:</b><br>"+ jqXHR.responseText);clearInterval(this.timer)}.bind(this)});if(phpvar.userdata)_getsubj()},get_anim:function(){_pop.hide();_kw_suggest.flg_done=false;this.$box.html(phpvar.loading);$.ajax({url:phpvar.ajaxurl,data:phpvar.postvar,cache:false,dataType:"json",success:function(json){this.$box.hide().html(json.out).slideDown("medium");this.$test.html(json.test).show()}.bind(this)})},page:function(p){phpvar.postvar.pg=p;this.get_anim()},mode:function(v){phpvar.postvar.list=v;phpvar.postvar.actab="display"; this.get_anim()},gmref:function(num){phpvar.postvar.gmref=true;phpvar.postvar.gmnum=num;this.timer=setInterval(function(){this.get()}.bind(this),2E3)}};function _getsubj(){$subjbox.load(phpvar.ajaxurl,{"id":phpvar.id,"subj":true})}function _hide(){_hdiv.oc("about",0);_hdiv.oc("query",0)}function _sample(i,o){$sicon.fadeTo(0,1);$(o).fadeTo(0,0.5);_idbox.set(i)} var _kw_suggest={flg_done:false,$box:null,get:function(id){if(this.flg_done)return;$("#kw_recom")._loadex({u:phpvar.ajaxurl,v:{"id":phpvar.id,"kw_recom":true}});this.flg_done=true},add:function(domobj){var txt_box,txt_btn,$btn=$(domobj);if(!this.$box)this.$box=$("#inp_filtkw");txt_box=this.$box.val();txt_btn=$btn.text();if(txt_box.indexOf(txt_btn)===-1){$btn.addClass("shine");this.$box.val(txt_box+(txt_box==""?"":" ")+txt_btn)}else{$btn.removeClass("shine");this.$box.val(txt_box.replace(txt_btn,"").replace(/ +/, " ").trim())}}}; var _dbid={vals:{},$box_inc:"",$box_exc:"",getitems:function(id){var $div=$("#func_items");$div.text()||$div._loadex({u:phpvar.ajaxurl,v:{"id":id,"dbid":true}})},filt:function(key,obj){_pop.hide(2);var num=$(obj).val();$trg=$(".poptrg_act");this.$box_inc=this.$box_inc||$("#inp_dbid_inc");this.$box_exc=this.$box_exc||$("#inp_dbid_exc");if(num==1){$trg.addClass("filt_inc");this.$box_inc.val(this.$box_inc.val()+" "+key)}else{$trg.removeClass("filt_inc");this.$box_inc.val(this.$box_inc.val().replace(key,"").replace(/ +/, " ").trim())}if(num==2){$trg.addClass("filt_exc");this.$box_exc.val(this.$box_exc.val()+" "+key)}else{$trg.removeClass("filt_exc");this.$box_exc.val(this.$box_exc.val().replace(key,"").replace(/ +/," ").trim())}}}; </script>