EMDB < EMD-42926

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entry_container"> <div class="entry_header_button"> <a id="entry_header_click_pc"><i class="fas fa-caret-up header_button"></i></a> </div> <div class="entry_header_container"> <h4>EMD-42926</h4> <b>Helical reconstruction</b><br> <b>4.27 Å</b><br> <a id="fresco0" href="https://www.ebi.ac.uk/emdb/images/entry/EMD-42926/400_42926.gif" class="fresco" data-fresco-caption="EMD-42926" data-fresco-group-options="loop: true" data-fresco-group="entry"> <img class="entry_image" src="https://www.ebi.ac.uk/emdb/images/entry/EMD-42926/400_42926.gif" alt="EMD-42926" onerror="this.src='/em_static/emdb/emdb_no_image.png'"/> </a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_xsurface.jpeg" class="fresco" data-fresco-caption="3D surface of the primary map viewed along the X-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_ysurface.jpeg" class="fresco" data-fresco-caption="3D surface of the primary map viewed along the Y-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_zsurface.jpeg" class="fresco" data-fresco-caption="3D surface of the primary map viewed along the Z-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_xprojection.jpeg" class="fresco" data-fresco-caption="Orthogonal projection of the map along the X-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_yprojection.jpeg" class="fresco" data-fresco-caption="Orthogonal projection of the map along the Y-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_zprojection.jpeg" class="fresco" data-fresco-caption="Orthogonal projection of the map along the Z-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_glow_xstd.jpeg" class="fresco" data-fresco-caption="Orthogonal standard-deviation projection of the map along the X-axis (False-colour)" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_glow_ystd.jpeg" class="fresco" data-fresco-caption="Orthogonal standard-deviation projection of the map along the Y-axis (False-colour)" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_glow_zstd.jpeg" class="fresco" data-fresco-caption="Orthogonal standard-deviation projection of the map along the Z-axis (False-colour)" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_xcentral_slice.jpeg" class="fresco" data-fresco-caption="Central slice through the map perpendicular to the X-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_ycentral_slice.jpeg" class="fresco" data-fresco-caption="Central slice through the map perpendicular to the Y-axis" data-fresco-group="entry"></a> <a href="https://www.ebi.ac.uk/pdbe/emdb-entry/emdbva/va-42926/va/emd_42926.map_scaled_zcentral_slice.jpeg" class="fresco" data-fresco-caption="Central slice through the map perpendicular to the Z-axis" data-fresco-group="entry"></a> <div class="header_buttons"> <a href="/emdb/EMD-42926?tab=3dview" title="Access the 3D visualisation of this entry." class="button"><i class="icon icon-common icon-cube"></i> 3D View</a> <a id="gallery_click_pc" class="button fresco" title="Access the gallery of image for this entry."><i class="fas fa-images"></i> Gallery</a> </div> <b>Deposition:</b> 23/11/2023<br> <b>Map released:</b> 27/11/2024<br> <b>Last modified:</b> 27/11/2024<br> </div> <div class="entry_small_submenu entry_submenu margin-top-large"> <a name="?tab=overview"><span name="?tab=overview" class="small_submenu_e submenu_e-selected ">Overview</span></a> <a name="?tab=3dview"><span name="?tab=3dview" class="small_submenu_e ">3D View</span></a> <a name="?tab=sample"><span name="?tab=sample" class="small_submenu_e ">Sample</span></a> <a name="?tab=experiment"><span name="?tab=experiment" class="small_submenu_e ">Experiment</span></a> <a name="?tab=validation"><span name="?tab=validation" class="small_submenu_e ">Validation</span></a> <a name="?tab=volume"><span name="?tab=volume" class="small_submenu_e ">Volume Browser</span></a> <a name="?tab=interpretation"><span name="?tab=interpretation" class="small_submenu_e ">Additional data</span></a> <a name="?tab=links"><span name="?tab=links" class="small_submenu_e ">Links</span></a> </div> </div> </div> <div id="entry_area" class="small-12 medium-8 large-9 column card-right"> <div id="entry_submenu" class="entry_submenu"> <a name="?tab=overview"><span name="?tab=overview" class="submenu_e submenu_e-selected ">Overview</span></a> <a name="?tab=3dview"><span name="?tab=3dview" class="submenu_e ">3D View</span></a> <a name="?tab=sample"><span name="?tab=sample" class="submenu_e ">Sample</span></a> <a name="?tab=experiment"><span name="?tab=experiment" class="submenu_e ">Experiment</span></a> <a name="?tab=validation"><span name="?tab=validation" class="submenu_e ">Validation</span></a> <a name="?tab=volume"><span name="?tab=volume" class="submenu_e ">Volume Browser</span></a> <a name="?tab=interpretation"><span name="?tab=interpretation" class="submenu_e ">Additional data</span></a> <a name="?tab=links"><span name="?tab=links" class="submenu_e ">Links</span></a> </div> <div id="entry_main_header"> <span class="float-left"><h3 class="entry_id">EMD-42926</h3></span> <span> <div class="float-right"> <a id="download_click" class="button dropbtn">Download <i class="fas fa-sort-down margin-left-medium"></i></a> <div id="download_menu" class="dropdown-content"> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-42926/map/emd_42926.map.gz">3D volume (map.gz)</a> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-42926/header/emd-42926-v30.xml">Experimental metadata (xml)</a> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-42926/metadata/emd-42926.cif.gz">Experimental Metadata (cif.gz)</a> <hr class="no-margin"> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/EMD-42926/emd_42926_validation.pdf.gz">Map-only Validation report (pdf.gz)</a> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/EMD-42926/emd_42926_validation.cif.gz">Map-only Validation report (cif.gz)</a> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/EMD-42926/emd_42926_validation.xml.gz">Map-only Validation report (xml.gz)</a> <hr class="no-margin"> <a href="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emicss/entries/42/9/42926/emd_42926_emicss.xml">EMICSS annotations (xml)</a> </div> </div> </span> </div> <div id="entry_main_content"> <h4 class="emdb_title">Cellular CHMP1B/IST1 filament - Class Id</h4> <div class="show-for-small-only entry_container"> <div class="entry_header_button"> <a id="entry_header_click_mobile"><i class="fas fa-caret-up header_button"></i></a> </div> <div class="entry_header_container"> <h4>EMD-42926</h4> <b>Helical reconstruction</b><br> <b>4.27 Å</b><br> <img class="entry_image" src="https://www.ebi.ac.uk/emdb/images/entry/EMD-42926/400_42926.gif" alt="EMD-42926" onerror="this.src='/em_static/emdb/emdb_no_image.png'"/> <div class="header_buttons"> <a href="/emdb/EMD-42926?tab=3dview" title="Access the 3D visualisation of this entry." class="button"><i class="icon icon-common icon-cube"></i> 3D View</a> <a id="gallery_click_mobile" class="button fresco" title="Access the gallery of image for this entry."><i class="fas fa-images"></i> Gallery</a> </div> <b>Deposition:</b> 23/11/2023<br> <b>Map released:</b> 27/11/2024<br> <b>Last modified:</b> 27/11/2024<br> </div> <div class="entry_small_submenu entry_submenu margin-top-large"> <a name="?tab=overview"><span name="?tab=overview" class="small_submenu_e submenu_e-selected ">Overview</span></a> <a name="?tab=3dview"><span name="?tab=3dview" class="small_submenu_e ">3D View</span></a> <a name="?tab=sample"><span name="?tab=sample" class="small_submenu_e ">Sample</span></a> <a name="?tab=experiment"><span name="?tab=experiment" class="small_submenu_e ">Experiment</span></a> <a name="?tab=validation"><span name="?tab=validation" class="small_submenu_e ">Validation</span></a> <a name="?tab=volume"><span name="?tab=volume" class="small_submenu_e ">Volume Browser</span></a> <a name="?tab=interpretation"><span name="?tab=interpretation" class="small_submenu_e ">Additional data</span></a> <a name="?tab=links"><span name="?tab=links" class="small_submenu_e ">Links</span></a> </div> </div> <div id="entry_general"> <div id="entry_basic"> <b>Sample Organism:</b> <a href='/emdb/search/?q=natural_source_ncbi_code:"9606"'>Homo sapiens</a> <br> <b>Sample:</b> <a href='/emdb/search/?q=sample_name:"CHMP1B/IST1 copolymer isolated and purified from HeLa cell over expression"'>CHMP1B/IST1 copolymer isolated and purified from HeLa cell over expression</a><br> <span id="emdb_pub"></span> <span id="bionotes"></span> <span id="raw_data"></span> <br> <b>Deposition Authors: </b> <a href='/emdb/search/?q=author:"Talledge N"'>Talledge N</a> <a class="no-underline" href="https://orcid.org/0000-0002-4603-0120" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0002-4603-0120"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Laughlin TG"'>Laughlin TG</a> <a class="no-underline" href="https://orcid.org/0000-0001-8943-1330" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0001-8943-1330"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Alian A"'>Alian A</a> <a class="no-underline" href="https://orcid.org/0000-0003-1901-3832" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0003-1901-3832"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"McCullough J"'>McCullough J</a> <a class="no-underline" href="https://orcid.org/0000-0001-6836-4394" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0001-6836-4394"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a> </div> <div id="entry_publication"> <b class="publication_title font-larger"> <a href="#" target="_blank" id="entry_publication_link"> <i class="icon icon-generic" data-icon="P"></i> ESCRT-III Assembles Around Mis-segregated DNA to Engage NoCut<sup><i class="icon icon-common icon-external-link-alt"></i></sup> </a> </b> <div class="pub_citation margin-top-large"> <a href='/emdb/search/?q=author:"Talledge N"'>Talledge N</a> <a class="no-underline" href="https://orcid.org/0000-0002-4603-0120" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0002-4603-0120"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Glover J"'>Glover J</a>, <a href='/emdb/search/?q=author:"McCullough J"'>McCullough J</a> <a class="no-underline" href="https://orcid.org/0000-0001-6836-4394" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0001-6836-4394"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Alian A"'>Alian A</a> <a class="no-underline" href="https://orcid.org/0000-0003-1901-3832" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0003-1901-3832"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Sadler JBA"'>Sadler JBA</a>, <a href='/emdb/search/?q=author:"Dempsey N"'>Dempsey N</a>, <a href='/emdb/search/?q=author:"Laughlin TG"'>Laughlin TG</a> <a class="no-underline" href="https://orcid.org/0000-0001-8943-1330" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0001-8943-1330"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Nguyen HC"'>Nguyen HC</a> <a class="no-underline" href="https://orcid.org/0000-0002-6142-8807" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0002-6142-8807"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Wenzel D"'>Wenzel D</a> <a class="no-underline" href="https://orcid.org/0000-0002-3605-6220" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0002-3605-6220"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Lalonde MS"'>Lalonde MS</a>, <a href='/emdb/search/?q=author:"Ventimiglia LN"'>Ventimiglia LN</a>, <a href='/emdb/search/?q=author:"LaJoie D"'>LaJoie D</a>, <a href='/emdb/search/?q=author:"Iwasa J"'>Iwasa J</a> <a class="no-underline" href="https://orcid.org/0000-0002-4949-7607" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0002-4949-7607"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Starling T"'>Starling T</a>, <a href='/emdb/search/?q=author:"Padilla-Parra S"'>Padilla-Parra S</a>, <a href='/emdb/search/?q=author:"Ullman KS"'>Ullman KS</a> <a class="no-underline" href="https://orcid.org/0000-0003-3693-2830" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0003-3693-2830"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Frost A"'>Frost A</a> <a class="no-underline" href="https://orcid.org/0000-0003-2231-2577" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0003-2231-2577"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Sundquist WI"'>Sundquist WI</a> <a class="no-underline" href="https://orcid.org/0000-0001-9988-6021" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0001-9988-6021"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a>, <a href='/emdb/search/?q=author:"Martin-Serrano J"'>Martin-Serrano J</a> <a class="no-underline" href="https://orcid.org/0000-0002-8183-3914" target="_blank"><span class="basic-tooltip" data-tooltip tabindex="1" title="0000-0002-8183-3914"><img src="//www.ebi.ac.uk/web_guidelines/images/logos/orcid/orcid_16x16.png"></span></a> <br> To Be Published </div> <div id="references" class="margin-top-large"> </div> <div id="abstract_div" class="margin-top-large"> <div id="abstract" align="justify"></div> </div> </div> </div> </div> </div> </div> </section> </div>       <div id="advanced_search" class="reveal-modal-bg modal_box large"> <div class="modal-content"> <div class="modal-header"> <a id="adv_close_click"><span class="close">×</span></a> <p>Searching in <span class="bold padding-right-large">EMDB</span><a class="clickable_link" href="/emdb/documentation/search" target="_blank">Help <i class="icon icon-generic" data-icon="?"></i></a></p> </div> <form id="form_adv_search"> <div class="modal-body"> <div id="card_list"> </div> <div> Field: <div class="col_source"> <select id="adv_source" name="topic" class="js-example-basic-single"> <option selected disabled hidden style='display: none' value=''>Choose...</option> <optgroup label="General information"> <option value="emdb_id" data-type="string">EMDB ID</option> <option value="title" data-type="text">Title</option> <option value="author_name" data-type="text">Author</option> <option value="author_orcid" data-type="text">ORCID</option> <option value="structure_determination_method" data-type="list">EM method</option> <option value="current_status" data-type="list">Current status</option> <option value="deposition_date" data-type="date">Deposition date</option> <option value="release_date" data-type="date">Release date</option> <option value="deposition_site" data-type="list">Deposition site</option> <option value="last_processing_site" data-type="list">Last processing site</option> <option value="fitted_pdbs" data-type="string">Fitted models</option> <option value="xref_EMPIAR" data-type="string">Raw data</option> <option value="resolution" data-type="float">Resolution</option> <option value="resolution_method" data-type="list">Resolution method</option> <option value="software" data-type="text">Software</option> <option value="composite_map" data-type="bool">Composite map</option> <option value="chembl_name" data-type="text">Ligand name</option> <option value="cpx_name" data-type="text">Complex name</option> <option value="pfam_name" data-type="text">Domain name</option> <option value="drugbank_name" data-type="text">Drug name</option> <option value="go_name" data-type="text">GO term name</option> <option value="interpro_name" data-type="text">InterPro term name</option> <option value="chebi_name" data-type="text">ChEBI term name</option> <option value="xref" data-type="string">External reference</option> </optgroup> <optgroup label="Publication information"> <option value="pubblication_title" data-type="text">Publication title</option> <option value="primary_citation_year" data-type="int">Publication year</option> <option value="primary_citation_journal_name" data-type="text">Journal</option> <option value="primary_citation_author" data-type="text">Publication author</option> </optgroup> <optgroup label="General sample information"> <option value="sample_type" data-type="list">Sample type</option> <option value="sample_name" data-type="text">Sample name</option> <option value="natural_source_organism" data-type="text">Organism</option> <option value="natural_source_ncbi_code" data-type="string">Organism (NCBI code)</option> <option value="natural_source_strain_organism" data-type="text">Strain</option> <option value="natural_source_organ" data-type="text">Organ</option> <option value="natural_source_tissue" data-type="text">Tissue</option> <option value="natural_source_cell" data-type="text">Cell</option> <option value="natural_source_organelle" data-type="text">Organelle</option> <option value="natural_source_cellular_location" data-type="text">Cellular Location</option> <option value="EC_number" data-type="string">E.C. number</option> <option value="molecular_weight_method" data-type="string">Molecular Weight method</option> <option value="assembly_molecular_weight" data-type="float">Molecular Weight (Da)</option> <option value="recombinant_exp_flag" data-type="bool">Recombinant Expression</option> <option value="recombinant_expression_organism" data-type="text">Recombinant organism</option> <option value="recombinant_expression_ncbi_code" data-type="string">Recombinant organism (NCBI code)</option> <option value="recombinant_expression_strain_organism" data-type="text">Recombinant strain</option> <option value="recombinant_expression_cell" data-type="text">Recombinant expression cell</option> <option value="recombinant_expression_plasmid" data-type="text">Recombinant expression plasmid</option> <option value="sample_classification" data-type="list">DNA/RNA classification</option> <option value="structure_type" data-type="string">DNA/RNA structure</option> </optgroup> <optgroup label="Validation Analysis"> <option value="estimated_volume_from_map_value" data-type="float">Estimated volume from the map</option> <option value="calculated_resolution_fsc_0143_value" data-type="float">Calculated resolution using FSC 0.143</option> <option value="calculated_resolution_fsc_05_value" data-type="float">Calculated resolution using FSC 0.5</option> <option value="calculated_resolution_fsc_halfbit_value" data-type="float">Calculated resolution using FSC half-bit</option> <option value="author_resolution_fsc_0143_value" data-type="float">Author-provided resolution using FSC 0.143</option> <option value="author_resolution_fsc_05_value" data-type="float">Author-provided resolution using FSC 0.5</option> <option value="author_resolution_fsc_halfbit_value" data-type="float">Author-provided resolution using FSC half-bit</option> <option value="map_model_resolution_fsc_05_value" data-type="float">Map-model resolution using FSC 0.5</option> <option value="overall_atom_inclusion_value" data-type="float">Overall atom inclusion</option> <option value="average_qscore_value" data-type="float">Average Q-Score</option> </optgroup> <optgroup label="Taxonomy"> <option value="species_name" data-type="text">Species</option> <option value="genus_name" data-type="text">Genus</option> <option value="family_name" data-type="text">Family</option> <option value="order_name" data-type="text">Order</option> <option value="class_name" data-type="text">Class</option> <option value="phylum_name" data-type="text">Phylum</option> <option value="kingdom_name" data-type="text">Kingdom</option> <option value="superkingdom_name" data-type="text">Super Kingdom</option> </optgroup> <optgroup label="Virus-specific sample information"> <option value="virus_serotype_organism" data-type="text">Serotype</option> <option value="virus_serocomplex_organism" data-type="text">Serocomplex</option> <option value="virus_category" data-type="list">Category</option> <option value="virus_isolate" data-type="list">Isolate</option> <option value="virus_enveloped" data-type="bool">Enveloped</option> <option value="virus_empty" data-type="bool">Empty</option> <option value="virus_natural_host_organism" data-type="text">Natural host organism</option> <option value="virus_natural_host_ncbi_code" data-type="string">Natural host organism (NCBI code)</option> <option value="virus_host_recombinant_organism" data-type="text">Host recombinant organism</option> <option value="virus_host_recombinant_ncbi_code" data-type="string">Host recombinant organism (NCBI code)</option> <option value="virus_host_recombinant_strain_organism" data-type="text">Host recombinant strain</option> <option value="virus_host_recombinant_strain_cell" data-type="text">Host recombinant cell</option> <option value="virus_host_recombinant_strain_plasmid" data-type="text">Host recombinant plasmid</option> <option value="virus_shell_name" data-type="text">Shell</option> <option value="virus_shell_triangulation_count" data-type="int">Shell triangulation</option> <option value="virus_shell_diameter" data-type="float">Shell diameter</option> </optgroup> <optgroup label="Structure determination: General"> <option value="structure_determination_method" data-type="list">Structure determination method</option> <option value="aggregation_state" data-type="list">Aggregation State</option> </optgroup> <optgroup label="Specimen preparation"> <option value="specimen_preparation_type" data-type="list">Specimen preparation type</option> <option value="buffer_ph_value" data-type="float">Buffer pH</option> <option value="buffer_component_formula" data-type="string">Buffer formula</option> <option value="buffer_component_name" data-type="text">Buffer name</option> <option value="staining_category" data-type="list">Staining type</option> <option value="staining_material" data-type="string">Staining material</option> <option value="grid_model" data-type="string">Grid model</option> <option value="grid_material" data-type="list">Grid material</option> <option value="grid_mesh_count" data-type="int">Grid mesh</option> <option value="film_material" data-type="list">Support film material</option> <option value="film_topology" data-type="list">Support film topology</option> <option value="film_thickness" data-type="float">Support film thickness</option> <option value="pretreatment_type" data-type="string">Pretreatment type</option> <option value="pretreatment_atmosphere" data-type="list">Pretreatment atmosphere</option> <option value="vitrification_cryogen_name" data-type="list">Cryogen</option> <option value="vitrification_chamber_humidity_value" data-type="float">Chamber humidity</option> <option value="vitrification_chamber_temperature" data-type="float">Chamber temperature</option> <option value="pretreatment_pressure_value" data-type="float">Vitrification pressure</option> <option value="vitrification_instrument" data-type="list">Vitrification instrument</option> <option value="vitrification_method" data-type="string">Vitrification method</option> </optgroup> <optgroup label="Crystal preparation"> <option value="crystallography_lipid_protein_value" data-type="float">Lipid protein ratio</option> <option value="crystallography_lipid_mixture_type" data-type="string">Lipid mixture</option> <option value="crystallography_instrument" data-type="string">Instrument</option> <option value="crystallography_atmosphere" data-type="string">Atmosphere</option> <option value="crystallography_temperature" data-type="float">Temperature</option> </optgroup> <optgroup label="Tomography preparation"> <option value="tomography_fiducial_type" data-type="string">Fiducial type</option> <option value="tomography_embedding_material" data-type="string">Embedding material</option> <option value="tomography_fiducial_manufacturer_type" data-type="string">Fiducial manufacturer</option> <option value="tomography_fiducial_diameter" data-type="float">Fiducial diameter</option> <option value="tomography_freezing_instrument" data-type="list">Freezing instrument</option> </optgroup> <optgroup label="Sectioning"> <option value="sectioning_type" data-type="list">Sectioning type</option> <option value="sectioning_instrument" data-type="string">Sectioning instrument</option> <option value="sectioning_temperature" data-type="float">Sectioning temperature</option> <option value="sectioning_final_thickness" data-type="float">Final thickness</option> <option value="sectioning_ion" data-type="list">Focused ion bean</option> <option value="sectioning_voltage" data-type="float">Ion bean Voltage</option> <option value="sectioning_current_value" data-type="float">Ion bean current</option> <option value="sectioning_dose_rate_value" data-type="float">Ion bean dose rate</option> <option value="sectioning_duration_value" data-type="float">Ion bean duration</option> </optgroup> <optgroup label="Microscopy"> <option value="microscope_name" data-type="list">Microscope name</option> <option value="illumination_mode" data-type="list">Illumination mode</option> <option value="imaging_mode" data-type="list">Imaging mode</option> <option value="electron_source" data-type="list">Electron source</option> <option value="acceleration_voltage" data-type="float">Acceleration voltage</option> <option value="c2_aperture_diameter" data-type="float">C2 aperture diameter</option> <option value="nominal_cs_value" data-type="float">Nominal CS</option> <option value="nominal_defocus_min_value" data-type="float">Nominal defocus (Min)</option> <option value="nominal_defocus_max_value" data-type="float">Nominal defocus (Max)</option> <option value="calibrated_defocus_min_value" data-type="float">Calibrated defocus (Min)</option> <option value="calibrated_defocus_max_value" data-type="float">Calibrated defocus (Max)</option> <option value="nominal_magnification_value" data-type="float">Nominal magnification</option> <option value="calibrated_magnification_value" data-type="float">Calibrated magnification</option> <option value="specimen_holder_model" data-type="list">Specimen holder model</option> <option value="cooling_holder_cryogen" data-type="list">Cooling holder cryogen</option> <option value="microscopy_min_temperature" data-type="float">Minimum temperature</option> <option value="microscopy_avg_temperature" data-type="float">Average temperature</option> <option value="microscopy_max_temperature" data-type="float">Maximum temperature</option> <option value="specimen_holder_name" data-type="text">Specimen holder</option> <option value="microscopy_min_tilt_angle" data-type="float">Minimum tilt angle</option> <option value="microscopy_max_tilt_angle" data-type="float">Maximum tilt angle</option> <option value="legacy_tilt_params" data-type="string">Legacy tilt params</option> <option value="phase_plate_type" data-type="string">Phase plate</option> <option value="energy_filter_name" data-type="text">Energy filter name</option> <option value="film_detector_model" data-type="list">Film or detector model</option> <option value="film_detector_category" data-type="list">Film/Detector category</option> <option value="detector_mode" data-type="list">Detector mode</option> <option value="scanner" data-type="list">Scanner</option> <option value="imaging_width" data-type="int">Imaging width</option> <option value="imaging_height" data-type="int">Imaging height</option> <option value="sampling_interval_value" data-type="float">Sampling interval</option> <option value="grids_imaged_count" data-type="int">Number of grids images</option> <option value="imaging_real_count" data-type="int">Number of real images</option> <option value="imaging_diffraction_count" data-type="int">Number of diffraction images</option> <option value="imaging_exposure_time" data-type="float">Imaging exposure time</option> <option value="electron_dose_per_image_value" data-type="float">Electron dose per image</option> <option value="tilt_series_axis1_min_angle" data-type="float">Tilt series minimum angle</option> <option value="tilt_series_axis1_max_angle" data-type="float">Tilt series maximum angle</option> <option value="crystallography_camera_length" data-type="float">Crystallography camera length</option> <option value="crystallography_tilt_angle" data-type="float">Crystallography tilt angle</option> </optgroup> <optgroup label="Image Processing"> <option value="image_reconstruction_point_group" data-type="string">Point group</option> <option value="image_reconstruction_algorithm" data-type="string">Algorithm</option> <option value="image_reconstruction_resolution" data-type="float">Reconstruction resolution</option> <option value="image_reconstruction_resolution_method" data-type="list">Reconstruction resolution method</option> <option value="image_reconstruction_classes_count" data-type="int">Number of classes</option> <option value="image_reconstruction_helical_delta_z_value" data-type="float">Helical delta Z</option> <option value="image_reconstruction_images_count" data-type="int">Number of images used</option> <option value="image_reconstruction_subtomograms_count" data-type="int">Number of subtomograms used</option> <option value="crystal_parameters_plane_group" data-type="string">Crystal plane group</option> <option value="crystal_parameters_space_group" data-type="string">Crystal space group</option> <option value="segment_selection_count" data-type="int">Number of selected segments</option> <option value="subtomogram_extraction_tomograms_count" data-type="int">Number of tomograms</option> <option value="final_two_d_classification_classes_count" data-type="int">Final 2D classification number of classes</option> <option value="final_three_d_classification_classes_count" data-type="int">Final 3D classification number of classes</option> <option value="final_three_d_classification_avreage_members_classes_value" data-type="float">Final 3D classification avg. members per classes</option> </optgroup> <optgroup label="Startup model"> <option value="startup_model_type" data-type="string">Startup model type</option> <option value="startup_EMDB_model" data-type="string">Startup EMDB model</option> <option value="startup_PDB_model" data-type="string">Startup PDB model</option> <option value="startup_insilico_model" data-type="string">Startup insilico model</option> </optgroup> <optgroup label="Crystallography statistics"> <option value="crystallography_intensities_count" data-type="int">Number of intensities measured</option> <option value="crystallography_structure_factores_count" data-type="int">Number of structure factors</option> <option value="crystallography_fourier_space_coverage" data-type="float">Fourier space coverage</option> <option value="crystallography_r_sym_value" data-type="float">R sym</option> <option value="crystallography_r_merge_value" data-type="float">R merge</option> <option value="crystallography_overall_phase_error_value" data-type="float">Overall phase error</option> <option value="crystallography_overall_phase_residual_value" data-type="float">Overall phase residual</option> <option value="crystallography_phase_error_rejection_value" data-type="float">Phase error rejection criteria</option> </optgroup> <optgroup label="Map"> <option value="map_size_kb" data-type="int">Map size (kB)</option> <option value="map_data_type" data-type="list">Data type</option> <option value="map_col" data-type="int">Col</option> <option value="map_row" data-type="int">Row</option> <option value="map_sec" data-type="int">Sec</option> <option value="map_cell_alpha" data-type="float">Cell alpha</option> <option value="map_cell_beta" data-type="float">Cell beta</option> <option value="map_cell_gamma" data-type="float">Cell gamma</option> <option value="map_fast_axis" data-type="list">Fast axis</option> <option value="map_medium_axis" data-type="list">Medium axis</option> <option value="map_slow_axis" data-type="list">Slow axis</option> <option value="map_minimum_value" data-type="float">Minimum</option> <option value="map_maximum_value" data-type="float">Maximum</option> <option value="map_average_value" data-type="float">Average</option> <option value="map_std_value" data-type="float">Std</option> <option value="map_pixel_spacing_x" data-type="float">Voxel size X</option> <option value="map_pixel_spacing_y" data-type="float">Voxel size Y</option> <option value="map_pixel_spacing_z" data-type="float">Voxel size Z</option> </optgroup> <optgroup label="Modelling"> <option value="initial_model" data-type="string">Initial model</option> <option value="final_model" data-type="string">Final model</option> <option value="modelling_refinement_protocol" data-type="list">Modelling refining protocol</option> </optgroup> <optgroup label="Segmentation mask"> <option value="segmentation_filename" data-type="bool">Mask file</option> <option value="segmentation_mask_space_group" data-type="string">Space group</option> <option value="segmentation_mask_point_group" data-type="string">Point group</option> <option value="segmentation_mask_data_type" data-type="list">Data type</option> <option value="segmentation_mask_dimension_col" data-type="int">Dimension Col</option> <option value="segmentation_mask_dimension_row" data-type="int">Dimension Row</option> <option value="segmentation_mask_dimension_sec" data-type="int">Dimension Sec</option> <option value="segmentation_mask_cell_alpha" data-type="float">Cell alpha</option> <option value="segmentation_mask_cell_beta" data-type="float">Cell beta</option> <option value="segmentation_mask_cell_gamma" data-type="float">Cell gamma</option> <option value="segmentation_mask_fast_axis" data-type="list">Fast axis</option> <option value="segmentation_mask_medium_axis" data-type="list">Medium axis</option> <option value="segmentation_mask_slow_axis" data-type="list">Slow axis</option> <option value="segmentation_mask_minimum_value" data-type="float">Minimum</option> <option value="segmentation_mask_maximum_value" data-type="float">Maximum</option> <option value="segmentation_mask_average_value" data-type="float">Average</option> <option value="segmentation_mask_std_value" data-type="float">Std</option> <option value="segmentation_mask_pixel_spacing_x" data-type="float">Voxel size X</option> <option value="segmentation_mask_pixel_spacing_y" data-type="float">Voxel size Y</option> <option value="segmentation_mask_pixel_spacing_z" data-type="float">Voxel size Z</option> </optgroup> <optgroup label="Additional Map"> <option value="additional_map_filename" data-type="bool">Additional map file</option> <option value="additional_map_space_group" data-type="string">Space group</option> <option value="additional_map_point_group" data-type="string">Point group</option> <option value="additional_map_data_type" data-type="list">Data type</option> <option value="additional_map_dimension_col" data-type="int">Dimension Col</option> <option value="additional_map_dimension_row" data-type="int">Dimension Row</option> <option value="additional_map_dimension_sec" data-type="int">Dimension Sec</option> <option value="additional_map_cell_alpha" data-type="float">Cell alpha</option> <option value="additional_map_cell_beta" data-type="float">Cell beta</option> <option value="additional_map_cell_gamma" data-type="float">Cell gamma</option> <option value="additional_map_fast_axis" data-type="list">Fast axis</option> <option value="additional_map_medium_axis" data-type="list">Medium axis</option> <option value="additional_map_slow_axis" data-type="list">Slow axis</option> <option value="additional_map_minimum_value" data-type="float">Minimum</option> <option value="additional_map_maximum_value" data-type="float">Maximum</option> <option value="additional_map_average_value" data-type="float">Average</option> <option value="additional_map_std_value" data-type="float">Std</option> <option value="additional_map_pixel_spacing_x" data-type="float">Voxel size X</option> <option value="additional_map_pixel_spacing_y" data-type="float">Voxel size Y</option> <option value="additional_map_pixel_spacing_z" data-type="float">Voxel size Z</option> </optgroup> <optgroup label="Half Map"> <option value="half_map_filename" data-type="bool">Half map file</option> <option value="half_map_space_group" data-type="string">Space group</option> <option value="half_map_point_group" data-type="string">Point group</option> <option value="half_map_data_type" data-type="list">Data type</option> <option value="half_map_dimension_col" data-type="int">Dimension Col</option> <option value="half_map_dimension_row" data-type="int">Dimension Row</option> <option value="half_map_dimension_sec" data-type="int">Dimension Sec</option> <option value="half_map_cell_alpha" data-type="float">Cell alpha</option> <option value="half_map_cell_beta" data-type="float">Cell beta</option> <option value="half_map_cell_gamma" data-type="float">Cell gamma</option> <option value="half_map_fast_axis" data-type="list">Fast axis</option> <option value="half_map_medium_axis" data-type="list">Medium axis</option> <option value="half_map_slow_axis" data-type="list">Slow axis</option> <option value="half_map_minimum_value" data-type="float">Minimum</option> <option value="half_map_maximum_value" data-type="float">Maximum</option> <option value="half_map_average_value" data-type="float">Average</option> <option value="half_map_std_value" data-type="float">Std</option> <option value="half_map_pixel_spacing_x" data-type="float">Voxel size X</option> <option value="half_map_pixel_spacing_y" data-type="float">Voxel size Y</option> <option value="half_map_pixel_spacing_z" data-type="float">Voxel size Z</option> </optgroup> <optgroup label="Software"> <option value="microscopy_software" data-type="text">Microscopy</option> <option value="image_reconstruction_software" data-type="text">Final reconstruction</option> <option value="ctf_correction_software" data-type="text">CTF correction</option> <option value="molecular_replacement_software" data-type="text">Molecular replacement</option> <option value="symmetry_determination_software" data-type="text">Symmetry determination</option> <option value="merging_software" data-type="text">Merging</option> <option value="segment_selection_software" data-type="text">Segment selection</option> <option value="initial_angle_assignment_software" data-type="text">Initial angle assignment</option> <option value="final_angle_assignment_software" data-type="text">Final angle assignment</option> <option value="subtomogram_extraction_software" data-type="text">Subtomogram extraction</option> <option value="final_three_d_classification_software" data-type="text">Final 3D classification</option> <option value="lattice_distortion_correction_software" data-type="text">Lattice distortion correction</option> <option value="modelling_software" data-type="text">Modelling</option> </optgroup> <optgroup label="EMPIAR-specific fields"> <option value="empiar_id" data-type="string">EMPIAR ID</option> <option value="entry_doi" data-type="string">Entry DOI</option> <option value="organization" data-type="text">Organization</option> <option value="organization_category" data-type="list">Organization type</option> <option value="dataset_size_GB" data-type="float">Dataset (GB)</option> <option value="experimentType" data-type="list">Experiment type</option> <option value="scale" data-type="list">scale</option> <option value="exp_type" data-type="list">Entry type</option> <option value="image_set_category" data-type="list">Imageset category</option> <option value="xref_EMDB" data-type="string">Related EMDBs</option> <option value="workflow_file" data-type="string">Workflow file</option> <option value="image_set_header_format" data-type="list">Header format</option> <option value="image_set_data_format" data-type="list">Data format</option> <option value="image_set_num_images" data-type="int">Number of images</option> <option value="image_set_fpi" data-type="int">Frames per image</option> <option value="image_set_voxel_type" data-type="list">Voxel type</option> <option value="image_set_img_width" data-type="int">Image width</option> <option value="image_set_pixel_width" data-type="float">Pixel width</option> <option value="image_set_img_height" data-type="int">Image height</option> <option value="image_set_pixel_height" data-type="float">Pixel height</option> <option value="segmentation_file" data-type="string">Segmentation file</option> <option value="segmentation_original_format" data-type="list">Segmentation format</option> </optgroup> <optgroup label="External References (ID)"> <option value="xref_DOI" data-type="string">DOI</option> <option value="xref_PUBMED" data-type="string">Pubmed</option> <option value="xref_ISSN" data-type="string">ISSN</option> <option value="xref_ASTM" data-type="string">ASTM</option> <option value="xref_UNIPROTKB" data-type="string">UniprotKb</option> <option value="xref_PDBEKB" data-type="string">PDBe-KB</option> <option value="xref_ALPHAFOLD" data-type="string">AlphaFold DB</option> <option value="xref_UNIPARC" data-type="string">Uniparc</option> <option value="xref_INTERPRO" data-type="string">INTERPRO</option> <option value="xref_GO" data-type="string">GO</option> <option value="xref_CPX" data-type="string">Complex Portal</option> <option value="xref_PFAM" data-type="string">Pfam</option> <option value="xref_CATH" data-type="string">CATH</option> <option value="xref_SCOP" data-type="string">SCOP</option> <option value="xref_REFSEQ" data-type="string">Refseq</option> <option value="xref_GENBANK" data-type="string">Genbank</option> <option value="xref_CAS" data-type="string">CAS</option> <option value="xref_PUBCHEM" data-type="string">PubChem</option> <option value="xref_DRUGBANK" data-type="string">DrugBank</option> <option value="xref_CHEBI" data-type="string">CHEBI</option> <option value="xref_CHEMBL" data-type="string">CHEMBL</option> <option value="xref_CARDBANK" data-type="string">CARDBANK</option> <option value="xref_BIA" data-type="string">BioImage Archive</option> <option value="xref_IDR" data-type="string">IDR</option> </optgroup> </select> </div> </div> </div> <div class="modal-footer"> <a id="adv_search_click" class="button right" title="Search on EMDB.">Search</a> </div> </form> </div> </div> <div id="share_modal" class="reveal-modal-bg modal_box_share large"> <div class="modal-content"> <div class="modal-header"> <a id="close_share_modal"><span class="close">×</span></a> <p>Share EMDB</p> </div> <div class="modal-body">  <a id="share_facebook" title="Share this page on Facebook." class="resp-sharing-button__link" href="https://facebook.com/sharer/sharer.php?u=https%3A%2F%2Femdb-empiar.org%2F" target="_blank" rel="noopener" aria-label=""> <div class="resp-sharing-button 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async="" src="/em_static/emdb/analytics.js"></script> <script src="/em_static/emdb/jquery.min.js"></script> <script src="/em_static/emdb/jquery-ui.min.js"></script> <script src="/em_static/select2-4.0.13/dist/js/select2.min.js"></script> <script src="/em_static/select2-4.0.13/dist/js/placeholder.js"></script>  <script defer="defer" src="/em_static/emdb/script.js"></script>  <script src="/em_static/emdb/foundation.js"></script> <script src="/em_static/emdb/foundationExtendEBI.js"></script> <script>$(document).foundation();</script> <script>$(document).foundationExtendEBI();</script> <style id="dynamic-stuck-height"> .masthead.sticky.is-stuck { margin-top: -151px !important; } </style>  <script src="/em_static/foundation-datepicker/js/foundation-datepicker.js"></script> <script src="/em_static/foundation-datepicker/js/locales/foundation-datepicker.vi.js"></script> <script src="/em_static/emdb/custom.js"></script> <script src="/em_static/sequence-viewer/sequence-viewer.min.js"></script> <script src="/em_static/cytoscape-js/cytoscape.min.js"></script> <script src="/em_static/cytoscape-js/dagre.js"></script> <script src="/em_static/cytoscape-js/cytoscape-dagre.js"></script> <script src="/em_static/cytoscape-js/cytoscape-node-html-label.min.js"></script> <script src="/em_static/fresco-2.3.0/dist/js/fresco.min.js"></script> <script src="/em_static/bioseq/bioseq.min.js"></script> <script> var globalSequences; /** * Display AlphaFold links if there's a model for the sample **/ function appendAlphaFold(){ $('.alphafold').each(function(i, obj) { let uniprot_id = $(obj).attr('title'); $.ajax({ type: 'GET', url: `https://alphafold.ebi.ac.uk/api/prediction/${uniprot_id}`, success: function() { $(obj).removeClass("hide"); } }); }); } /** * Convert MW value from Dalton the most appropiated unit * @param {Float} value Value in Da * @return {String} Text value including the most appropriated unit **/ function convertDa(value) { if(value < 1000){ return `${value} Da`; }else if (value < 1000000){ value /= 1000; value = parseInt(value); return `${value} kDa` }else{ value /= 1000000; value = parseInt(value); return `${value} MDa` } } /** * Fetch and append the overall molecular weight of the entry **/ function appendMW(){ let emdb_id = "EMD-42926"; let query = `emdb_id:"${emdb_id}"`; let URL = "/emdb/api/search/$000000$".replace('$000000$', query); URL += "?rows=1&fl=assembly_molecular_weight&wt=csv"; $.ajax({ type: 'GET', url: URL, dataType: "text", success: function(result) { let rows = result.split('\n'); if(!isNaN(rows[1])){ let mw = parseFloat(rows[1]); mw = convertDa(mw); let html_line = `<b>Overall Molecular Weight:</b> ${mw} (Calculated from the model)<br>`; $("#overall_mw").append(html_line); } } }); } /** * Check if the given file exists **/ function fileExists(url) { let http = new XMLHttpRequest(); http.open('HEAD', url, false); try { http.send(); } catch (error) { return false; } return http.status !== 404; } /** * Open and close download dropdown menu **/ function download_click() { document.getElementById("download_menu").classList.toggle("show"); } /** * Close the download dropdown menu by clicking outside. **/ window.onclick = function(event) { if (!event.target.matches('.dropbtn')) { let dropdowns = document.getElementsByClassName("dropdown-content"); for (let i = 0; i < dropdowns.length; i++) { let openDropdown = dropdowns[i]; if (openDropdown.classList.contains('show')) { openDropdown.classList.remove('show'); } } } }; /** * Initialize the sequence viewer package. It also find the number * of characaters per line according to the user's window size. **/ function intitialize_sequences() { globalSequences = {}; let window = $(document).width(); let chars_line = 50; if (window > 1175) { chars_line = 90; } else if (window > 1065) { chars_line = 80; } else if (window > 1023) { chars_line = 70; } else if (window > 935) { chars_line = 60; } else if (window > 810) { chars_line = 50; } else if (window > 680) { chars_line = 40; } else if (window > 639) { chars_line = 30; } else if (window > 615) { chars_line = 60; } else if (window > 530) { chars_line = 50; } else if (window > 440) { chars_line = 40; } else if (window > 360) { chars_line = 30; } else { chars_line = 20; } for (let i = 0; i < $(".sequence").length; i++) { let seq_div = $(".sequence")[i]; let id = $(seq_div).attr('id'); let sequence = $(seq_div).data('sequence'); sequence = sequence.replace(/(\s)/gm, ""); sequence = sequence.replace(/($.*?$)/gm, "X"); if (sequence.length > 0) { let seq_obj = new Sequence(sequence); seq_obj.render('#' + id, { 'showLineNumbers': true, 'wrapAminoAcids': true, 'charsPerLine': chars_line, 'toolbar': false, 'search': false, 'title': "Sequence", 'sequenceMaxHeight': "100%", 'badge': false }); let molId = $(`#${id}`).closest(".macromolecule-sample").attr("id"); globalSequences[molId] = seq_obj; } } } /** * Decode HTML strings * @param {String} input String that may contain HTML tags * @return {String} decoded text **/ function htmlDecode(input){ let e = document.createElement('textarea'); e.innerHTML = input; // handle case of empty input return e.childNodes.length === 0 ? "" : e.childNodes[0].nodeValue; } /** * Call the Europe PMC API to obtain the abstract of the publication * and append it to the entry page. **/ function fetchAbstract() { let URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=ext_id:%20src%3Amed&resultType=core&cursorMark=*&pageSize=1&format=xml"; } /** * Sort given table by given ID. * @param {String} table_id table ID * @param {Int} sortColumn column number **/ function sortTable(table_id, sortColumn){ let tableData = document.getElementById(table_id).getElementsByTagName('tbody').item(0); let rowData = tableData.getElementsByTagName('tr'); for(let i = 0; i < rowData.length - 1; i++){ for(let j = 0; j < rowData.length - (i + 1); j++){ if(Number(rowData.item(j).getElementsByTagName('td').item(sortColumn).innerHTML.replace(/[^0-9\.]+/g, "")) > Number(rowData.item(j+1).getElementsByTagName('td').item(sortColumn).innerHTML.replace(/[^0-9\.]+/g, ""))){ tableData.insertBefore(rowData.item(j+1),rowData.item(j)); } } } } /** * Access the EMDB API to retrieve the entries that share the same publication. * The data is then formatted and appended to the page. **/ function emdbsBypublication() { let URL = ""; if(URL === ""){ if($("#table-emdb-rel tbody tr").length === 0){ $("#rel-entries").empty(); } return; } if (URL.length > 0) { $.ajax({ url: URL, headers: { 'Content-Type': 'application/x-www-form-urlencoded' }, type: "GET", dataType: "text", crossDomain: true, data: {}, success: function (result) { let content = result.trim().split("\n"); for (let i = 1; i < content.length; i++) { let elem_id = `row-rel-${content[i]}`; let row = document.getElementById(elem_id); if(row){ let col = $(`#${elem_id} .col-rel-relationship`); let text = col.html().trim(); col.empty(); col.append(text + "/Publication"); }else{ let url = "/emdb/EMD-00000".replace('00000', content[i].substr(4)); $.ajax({ url : url, type : "get", async: false, success : function() { let html = `<tr id="row-rel-${content[i]}"> <td><a href="${url}">${content[i]}</a></td> <td class="text-center col-rel-relationship">Publication</td> <td class="col-rel-details"></td> </tr>`; $("#table-emdb-rel tbody").append(html); } }); } } }, error: function () { console.log("Failed to connect to Europe PMC."); }, complete: function () { if($("#table-emdb-rel tbody tr").length === 0){ $("#rel-entries").empty(); }else{ sortTable("table-emdb-rel", 0); } } }); } } /** * Find related entries based on GO and InterPro **/ function emdbsBysimilarity() { const URL = "/emdb/api/emicss/similarities/EMD-42926"; if (URL.length > 0) { $.ajax({ url: URL, headers: { 'Content-Type': 'application/x-www-form-urlencoded' }, type: "GET", dataType: "json", data: {}, success: function (result) { const entries = result['entries']; if (entries.length > 0){ let html = ` <div class="sim_map_header bottom-line height40"> <b class="font-larger float-left"><i class="fas fa-database"></i> Similar entries</b> <a class="accordion" data-parent="sim_map_content"><i class="fas fa-caret-up controls_button"></i></a> </div> <div id="sim_map_content" class="sim_map_content margin-top20 margin-left20"> <table> <thead> <th class="emdb-id-col">Entry</th> <th>Title</th> <th>Similarity</th> </thead> <tbody> `; for(let i = 0; i < entries.length; i++){ const emdb_id = entries[i]['emdb_id']; const title = entries[i]['title']; const similarity = entries[i]['similarity']; const link = "/emdb/EMD-00000".replace('00000', emdb_id.substr(4)); html += ` <tr> <td><a href="${link}" target="_blank">${emdb_id}</a></td> <td>${title}</td> <td>${similarity}</td> </tr>`; } html += ` </tbody> </table> </div> `; $("#similar-entries").append(html); } }, error: function () { console.log("Failed to connect the API."); } }); } } /** * Add links to domain labels **/ function addDomainLinks() { $(".yaxis").each(function (i, element){ let url = ""; let id = element.textContent; if(id.substring(0,2) === "PF"){ url = `https://pfam.xfam.org/family/${id}`; }else if(id.substring(0,3) === "IPR"){ url = `https://www.ebi.ac.uk/interpro/entry/InterPro/${id}`; }else if (!isNaN(id.replaceAll(".",""))){ url = `https://www.cathdb.info/version/latest/superfamily/${id}`; } if(id.length) { $(element).click(function () { window.open(url, '_blank'); }); element.classList.add("pointer"); } }); } /** * Generate a distinct color given a numeric id. * @param {Int} number Numeric id * @return {String} Return a color in the hsl pattern **/ function selectColor(number) { const hue = number * 137.508; // use golden angle approximation return `hsl(${hue},50%,75%)`; } /** * Fetch the domains data from the EMDB annotation API and generate the visualisation. **/ function populateDomains() { $.ajax({ url: `/emdb/api/annotations/EMD-42926`, headers: { 'Content-Type': 'application/x-www-form-urlencoded' }, type: "GET", dataType: "json", data: {}, success: function (result) { let annotations = result['macromolecules']; for (const sample_id in annotations) { let sample = annotations[sample_id]; if(sample['type'] === "protein") { let sample_annotations = sample['annotations']; let fv; let color = 0; if("PFAM" in sample_annotations || "CATH" in sample_annotations || "INTERPRO" in sample_annotations){ //Initialize protvista let sequence = $(`#${sample_id}`).find(".sequence").data("sequence"); sequence = sequence.replace(/(\s)/gm, ""); sequence = sequence.replace(/($.*?$)/gm, "X"); fv = new FeatureViewer(sequence, `#fv_${sample_id}`, { showAxis: true, showSequence: true, brushActive: true, toolbar:false, bubbleHelp:true, zoomMax:10 }); fv.onFeatureSelected(function (obj) { let detail = obj['detail']; let start = parseInt(detail['start'])-1; let end = parseInt(detail['end']); let color = selectColor(detail['id']); let seqObj = globalSequences[sample_id]; seqObj.selection(start, end, color); }); } if("PFAM" in sample_annotations) { let pfam_annotations = sample_annotations['PFAM']; pfam_annotations.forEach(function (pfam, i) { fv.addFeature({ name: pfam['id'], className: pfam['id'], color: selectColor(color), type: "rect", filter: "type1", data: [{x: pfam['start'], y: pfam['end'], id: color, description: pfam['title']}] }); color += 1; }); } if("INTERPRO" in sample_annotations) { let ipr_annotations = sample_annotations['INTERPRO']; let selColor = selectColor(color); ipr_annotations.forEach(function (ipr, i) { fv.addFeature({ name: ipr['id'], className: ipr['id'], color: selectColor(color), type: "rect", filter: "type1", data: [ {x: ipr['start'], y: ipr['end'], id: color, description: ipr['title']} ] }); color += 1; }); } if("CATH" in sample_annotations) { let cath_annotations = sample_annotations['CATH']; let selColor = selectColor(color); cath_annotations.forEach(function (cath, i) { fv.addFeature({ name: cath['id'], className: `cath${cath['id'].replaceAll(".","_")}`, color: selectColor(color), type: "rect", filter: "type1", data: [ {x: cath['start'], y: cath['end'], id: color, description: cath['id']} ] }); color += 1; }); } } } addDomainLinks(); }, error: function () { $(".sample-domain").empty(); } }); } /** * Access the EMDB API to find raw data and avg. Q-Score. **/ function fetchAdditionalData(page="overview"){ let URL = `${emdb_root}/api/search/emdb_id:"EMD-42926"?wt=csv&download=false&fl=average_qscore,xref_EMPIAR`; $.ajax({ url: URL, headers: { 'Content-Type': 'application/x-www-form-urlencoded' }, type: "GET", dataType: "text", crossDomain: true, data: { }, success: function (result) { let content = result.trim().split("\n"); if(page === "overview"){ $("#raw_data").empty(); $("#qscore").empty(); if (content.length > 1 && content[1].length > 2){ let new_list = content[1].replaceAll('"','').split(','); content = Array.from(new Set(new_list)); let qscore = content[0]; if(qscore.length > 0){ $("#qscore").append(`(<b>Avg. Q-score:</b> ${qscore})`); } let empiar_list = content.slice(1) if(empiar_list[0].length > 0){ let new_content = `<b>Raw data: </b><a href="${project_root}/empiar/entry/${empiar_list[0].substr(7)}" target="_blank">${empiar_list[0]}</a>`; for(let i = 1; i < empiar_list.length; i++){ new_content += `, <a href="${project_root}/empiar/entry/${empiar_list[i].substr(7)}" target="_blank">${empiar_list[i]}</a>`; } new_content += "<br>" $("#raw_data").append(new_content); } } }else if(page === "links"){ $("#raw-data").empty(); if (content.length > 1 && content[1].length > 2){ let new_list = content[1].replaceAll('"','').split(','); content = Array.from(new Set(new_list)); let empiar_list = content.slice(1); empiar_list = empiar_list.filter(str => str.length > 0); if(empiar_list.length > 0){ let html = ` <div class="raw_header bottom-line height40"> <b class="font-larger float-left"><i class="fas fa-photo-video"></i> Raw data</b> <a id="raw-data-accordion" class="accordion" data-parent="raw_content"><i class="fas fa-caret-up controls_button"></i></a> </div> <div id="raw_content" class="raw_content margin-top20 margin-left20"> <table> <thead> <th>Accession</th> <th>EMPIAR</th> </thead> <tbody> `; for (const empId of empiar_list) { html += `<tr><td>${empId}</td><td class="text-center"><a href="${project_root}/empiar/entry/${empId.substr(7)}" target="_blank"><i class="icon icon-common icon-external-link-alt"></i></a></td></tr>`; } html += "</tbody></table></div>"; $("#raw-data").append(html); let element = document.getElementById("raw-data-accordion"); element.addEventListener('click', function () { control_div(this, "#raw_content"); }); } } } }, error: function () { $("#raw_data").empty(); } }); } /** * Set the given URL and page title in the browser * @param {String} HTML code fetched from the ajax call * @param {String} urlPath URL path **/ function setBrowserURL(data, urlPath){ urlPath = urlPath.split('#')[0]; let title = $(data).filter('title').text(); document.title = title; window.history.pushState({"pageTitle":title},"", urlPath); } /** * Implement the ajax-based navigation through the submenu in the entry page. **/ function ajaxNavigation() { $('.entry_submenu a').each((index,el) => { $(el).click((e) => { e.preventDefault(); let source_id = "#entry_general"; let target_id = "#entry_general"; let page_url = $(el).attr('name'); let original_url = page_url; let validation = false; $(".submenu_e").each(function() { if($(this).attr('name') === page_url){ $(this).addClass("submenu_e-selected") }else{ $(this).removeClass("submenu_e-selected") } }); $(".small_submenu_e").each(function() { if($(this).attr('name') === page_url){ $(this).addClass("submenu_e-selected") }else{ $(this).removeClass("submenu_e-selected") } }); if(page_url.includes("tab=validation")) { target_id = "#main-content-area_va"; page_url = `/emdb/va/42926/prodentry/`; validation = true; } if(page_url.includes("volume-browser")){ window.open(page_url, '_blank'); }else { $.ajax({ url: page_url, type: 'GET', beforeSend: function() { $(source_id).html(`<div class="emdb-loader center-div" style="margin-top: 3rem;"></div>`); }, success: (data) => { let tab = page_url.split("=")[1]; if (!tab){ tab = "VALIDATION"; } const ga_path = `/emdb/entry/#/${tab}`; //GA Track try{ gtag('event', 'page_view', { page_title: `EMDB < ${tab.toUpperCase()}`, page_path: ga_path, send_to: 'G-8QBZMP48RB' }) }catch (e){ console.log(e); } setBrowserURL(data, original_url); $(source_id).empty(); let fetched_data = $(data).find(target_id).html(); try{ $(source_id).append(fetched_data); }finally{ if(validation){ resetAccordion(); } } let urlParams = new URLSearchParams(page_url); setEventListener(); setReadMoreEvent(); if (urlParams.get('tab') === "overview") { fetchAbstract(); fetchAdditionalData(); }else if(urlParams.get('tab') === "sample"){ intitialize_sequences(); loadSampleNetwork(); appendAlphaFold(); appendMW(); populateDomains(); }else if(urlParams.get('tab') === "links"){ emdbsBypublication(); emdbsBysimilarity(); fetchAdditionalData("links"); linkCIF("42926"); } }, statusCode: { 500: function() { $(source_id).empty(); $(source_id).html("<p>An unexpected error occurred when attempting to display the " + "validation data for this entry. Please try again later or " + "<a href=\"//www.ebi.ac.uk/support/EMDB\">contact us</a>.</p>"); } } }) } }) }) } /** * Load the hierarchy tree between the samples into the Cytoscape.js * and append it into the entry page. **/ function loadSampleNetwork(){ let cy = window.cy = cytoscape({ container: document.getElementById('sample_graph'), boxSelectionEnabled: false, autounselectify: true, layout: {name: 'dagre'}, style: [ {selector: 'node',style: { "background-color": "white", "text-outline-color": "#555", "text-outline-width": "2px", "color": "#fff", "overlay-padding": "6px", 'border-color': '#000', 'border-width': 3, 'border-opacity': 0.5, "width": "data(size)", "height": "data(size)" } }, {selector: 'edge',style: { 'width': 4, 'target-arrow-shape': 'triangle', 'line-color': '#9dbaea', 'target-arrow-color': '#9dbaea', 'curve-style': 'bezier', 'overlay-opacity': 0 } } ], elements: { nodes: [{'data': {'id': 's1', 'name': 'complex_supramolecule', 'icon': '<i class="icon EMDB-Icon-set icon-EMDB_ProteinComplex"></i>', 'type': 0, 'degree': 4, 'size': 28, 'font': 18}}, {'data': {'id': 's2', 'name': 'complex_supramolecule', 'icon': '<i class="icon EMDB-Icon-set icon-EMDB_ProteinComplex"></i>', 'type': 0, 'degree': 2, 'size': 24, 'font': 16}}, {'data': {'id': 's3', 'name': 'complex_supramolecule', 'icon': '<i class="icon EMDB-Icon-set icon-EMDB_ProteinComplex"></i>', 'type': 0, 'degree': 2, 'size': 24, 'font': 16}}, {'data': {'id': 'm1', 'name': 'protein_or_peptide', 'icon': '<i class="icon icon-conceptual icon-structures"></i>', 'type': 1, 'degree': 2, 'size': 24, 'font': 16}}, {'data': {'id': 'm2', 'name': 'protein_or_peptide', 'icon': '<i class="icon icon-conceptual icon-structures"></i>', 'type': 1, 'degree': 2, 'size': 24, 'font': 16}}], edges: [{'data': {'source': 's1', 'target': 'm1'}}, {'data': {'source': 's1', 'target': 'm2'}}, {'data': {'source': 's1', 'target': 's2'}}, {'data': {'source': 's2', 'target': 'm1'}}, {'data': {'source': 's1', 'target': 's3'}}, {'data': {'source': 's3', 'target': 'm2'}}] } }); cy.nodeHtmlLabel([{ query: 'node', halign: 'center', valign: 'center', halignBox: 'center', valignBox: 'center', tpl: (data) => { return `<span style='font-size: ${data.font}px; padding-left: 8%'>${data.icon}</span>`; } }]); cy.maxZoom(3); cy.minZoom(0.5); cy.on('click', 'node', function(evt){ let node_id = $("#" + this.id()); $("#modal_body").empty(); node_id.clone().removeAttr("id").appendTo("#modal_body"); $("#header_text").empty(); let header_text = ""; if(this.id()[0] === 's') { header_text = node_id.closest(".supramolecule").find(".supra_header_text"); }else if(this.id()[0] === 'm'){ header_text = node_id.closest(".macromolecule").find(".macro_header_text"); } $(header_text).clone().appendTo("#header_text"); open_modal_id("#sample_details"); }); } /** * This function resets all the accordions panels in the page after it was appended * by an ajax call. **/ function resetAccordion(){ Foundation.addToJquery($); $(document).foundation(); //make sure the ajax has been finished and the HTML is properly set, otherwise move following line to you ajax success handler end. //$(document).foundation('reflow'); } /** * Add click evento to all the [show more] links in the entry page. **/ function setReadMoreEvent(){ $(".read-more").click(function(e) { e.preventDefault(); let t = $(this); t.parent().find('.more').removeClass('hidden'); t.addClass('hidden'); }); } /** * Minimize and expand the entry header on click. * @param {Object} e Minimize button object **/ function control_entry_header(e) { let div = $(e).closest(".entry_container").children(".entry_header_container"); let submenu = $(e).closest(".entry_container").children(".entry_small_submenu"); let icon = $(e).find(".header_button"); let box = $("#entry_box"); let area = $("#entry_area"); let entry_header_button = $(".entry_header_button"); if (div.css('display') === 'none') { div.show(); if ($(window).width() > 1180) { submenu.hide(); } else { submenu.show(); } box.removeClass("medium-1 large-1"); box.addClass("medium-4 large-3"); area.removeClass("medium-11 large-11"); area.addClass("medium-8 large-9"); icon.removeClass("fa-caret-down"); icon.addClass("fa-caret-up"); entry_header_button.css('text-align', 'right'); entry_header_button.css('margin-right', '15px'); } else { div.hide(); if ($(window).width() >= 640) { submenu.hide(); } icon.removeClass("fa-caret-up"); icon.addClass("fa-caret-down"); box.removeClass("medium-4 large-3"); box.addClass("medium-1 large-1"); area.removeClass("medium-8 large-9"); area.addClass("medium-11 large-11"); entry_header_button.css('text-align', 'center'); entry_header_button.css('margin-right', '0px'); } } /** * Add the event listeners related to the entry page **/ function setEventListener(){ document.getElementById('entry_header_click_pc').addEventListener("click", function () { control_entry_header(this); }); document.getElementById('entry_header_click_mobile').addEventListener("click", function () { control_entry_header(this); }); let elements = document.getElementsByClassName("accordion"); Array.from(elements).forEach(function (element) { let id = `#${element.dataset.parent}`; element.addEventListener('click', function () { control_div(this,id); }); }); elements = document.getElementsByClassName("modal-open"); Array.from(elements).forEach(function (element) { let id = `#${element.dataset.parent}`; element.addEventListener('click', function () { open_modal_id(id); }); }); elements = document.getElementsByClassName("modal-close"); Array.from(elements).forEach(function (element) { element.addEventListener('click', function () { close_emdb_modal(); }); }); } /** * Add the event listeners related to the entry page **/ function setRelEventListener(){ document.getElementById('download_click').addEventListener("click", download_click); document.getElementById('gallery_click_pc').addEventListener("click", function () { Fresco.show($('#fresco0')[0]); }); document.getElementById('gallery_click_mobile').addEventListener("click", function () { Fresco.show($('#fresco0')[0]); }); } /** * On the page ready, all the API calls are made, and the fetched data are * appended into the page **/ $(document).ready(function () { setEventListener(); setRelEventListener(); ajaxNavigation(); setReadMoreEvent(); $( document ).tooltip(); fetchAbstract(); fetchAdditionalData(); }); $(window).ajaxStop(function () { intitialize_sequences(); }); </script> </body> </html>

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EMDB < EMD-42926