{"EMPIAR-10612":{"imagesets":[{"segmentations":[],"name":"Unaligned movies in EER format of SARS-CoV-2 3a in MSP1E3D1 lipid nanodiscs - 1379 frames","directory":"data/200507-3a10ev_movies/1379_frames","category":"micrographs - multiframe","header_format":"EER","data_format":"EER","num_images_or_tilt_series":789,"frames_per_image":1379,"frame_range_min":null,"frame_range_max":null,"voxel_type":"BIT","pixel_width":0.3635,"pixel_height":0.3635,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"EER-format movies are in folders titled by total frame number. We recommend merging 30 frames for one dose fraction which gives 45 frame movies. The dose per frame is 0.0345 e/A2 (or 1.035e/A2 per suggested fraction). The gain reference image is in the movies folder. The super-resolution pixel size is 0.3635 A for a physical pixel size of 0.727 A. A cryosparc non-uniform refinement folder (containing polished particles) is also included.","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Unaligned movies in EER format of SARS-CoV-2 3a in MSP1E3D1 lipid nanodiscs - 1449 frames","directory":"data/200507-3a10ev_movies/1449_frames","category":"micrographs - multiframe","header_format":"EER","data_format":"EER","num_images_or_tilt_series":4809,"frames_per_image":1449,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.3635,"pixel_height":0.3635,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"EER-format movies are in folders titled by total frame number. We recommend merging 30 frames for one dose fraction which gives 48 frame movies. The dose per frame is 0.0345 e/A2 (or 1.035e/A2 per suggested fraction). The gain reference image is in the movies folder. The super-resolution pixel size is 0.3635 A for a physical pixel size of 0.727 A. A cryosparc non-uniform refinement folder (containing polished particles) is also included.","image_width":"4096","image_height":"4096"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"High-resolution SARS-CoV-2 ORF3a dimer in an MSP1E3D1 lipid nanodisc","principal_investigator":[{"author_orcid":"0000-0001-6768-3406","middle_name":"Graf","organization":"UC Berkeley","street":null,"town_or_city":"Berkeley","state_or_province":"California","post_or_zip":"94720","telephone":null,"fax":null,"first_name":"Stephen","last_name":"Brohawn","email":"brohawn [at] berkeley.edu","country":"United States","entry":"EMPIAR-10612"}],"status":"REL","deposition_date":"2020-11-28","release_date":"2021-02-05","obsolete_date":null,"update_date":"2023-02-20","corresponding_author":{"author":{"author_orcid":"0000-0001-6768-3406","middle_name":"Graf","organization":"UC Berkeley","street":null,"town_or_city":"Berkeley","state_or_province":"California","post_or_zip":"94720","first_name":"Stephen","last_name":"Brohawn","country":"United States"}},"authors":[{"author":{"name":"Kern DM","author_orcid":"0000-0001-8529-9045"}},{"author":{"name":"Hoel CM","author_orcid":"0000-0002-1344-0780"}},{"author":{"name":"Kotecha A","author_orcid":"0000-0002-4480-5439"}},{"author":{"name":"Brohawn SG","author_orcid":"0000-0001-6768-3406"}}],"cross_references":["","","","Error","500","{metadata={error-class=org.apache.solr.core.SolrCoreInitializationException,root-error-class=java.nio.file.NoSuchFileException},msg=SolrCore","'emdb'","is","not","available","due","to","init","failure:","Error","opening","new","searcher,trace=org.apache.solr.core.SolrCoreInitializationException:","SolrCore","'emdb'","is","not","available","due","to","init","failure:","Error","opening","new","searcher","at","org.apache.solr.core.CoreContainer.getCore(CoreContainer.java:1740)","at","org.apache.solr.servlet.HttpSolrCall.init(HttpSolrCall.java:253)","at","org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:538)","at","org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:419)","at","org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:351)","at","org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1602)","at","org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:540)","at","org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146)","at","org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)","at","org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257)","at","org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1711)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255)","at","org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1347)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203)","at","org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:480)","at","org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1678)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201)","at","org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1249)","at","org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144)","at","org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:220)","at","org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:152)","at","org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)","at","org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)","at","org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)","at","org.eclipse.jetty.server.Server.handle(Server.java:505)","at","org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:370)","at","org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:267)","at","org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305)","at","org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)","at","org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:126)","at","org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:366)","at","org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:781)","at","org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:917)","at","java.base/java.lang.Thread.run(Unknown","Source)","Caused","by:","org.apache.solr.common.SolrException:","Error","opening","new","searcher","at","org.apache.solr.core.SolrCore.<init>(SolrCore.java:1052)","at","org.apache.solr.core.SolrCore.<init>(SolrCore.java:881)","at","org.apache.solr.core.CoreContainer.createFromDescriptor(CoreContainer.java:1251)","at","org.apache.solr.core.CoreContainer.lambda$load$13(CoreContainer.java:765)","at","com.codahale.metrics.InstrumentedExecutorService$InstrumentedCallable.call(InstrumentedExecutorService.java:202)","at","java.base/java.util.concurrent.FutureTask.run(Unknown","Source)","at","org.apache.solr.common.util.ExecutorUtil$MDCAwareThreadPoolExecutor.lambda$execute$0(ExecutorUtil.java:210)","at","java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown","Source)","at","java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown","Source)","...","1","more","Caused","by:","org.apache.solr.common.SolrException:","Error","opening","new","searcher","at","org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:2162)","at","org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:2282)","at","org.apache.solr.core.SolrCore.initSearcher(SolrCore.java:1112)","at","org.apache.solr.core.SolrCore.<init>(SolrCore.java:993)","...","9","more","Caused","by:","org.apache.lucene.index.CorruptIndexException:","Problem","reading","index.","(resource=/var/solr/data/emdb/data/restore.20260811200813409/_90bku.fdt)","at","org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:144)","at","org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:84)","at","org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:177)","at","org.apache.lucene.index.ReadersAndUpdates.getReadOnlyClone(ReadersAndUpdates.java:219)","at","org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:109)","at","org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:526)","at","org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:116)","at","org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:92)","at","org.apache.solr.core.StandardIndexReaderFactory.newReader(StandardIndexReaderFactory.java:39)","at","org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:2126)","...","12","more","Caused","by:","java.nio.file.NoSuchFileException:","/var/solr/data/emdb/data/restore.20260811200813409/_90bku.fdt","at","java.base/sun.nio.fs.UnixException.translateToIOException(Unknown","Source)","at","java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown","Source)","at","java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown","Source)","at","java.base/sun.nio.fs.UnixFileSystemProvider.newFileChannel(Unknown","Source)","at","java.base/java.nio.channels.FileChannel.open(Unknown","Source)","at","java.base/java.nio.channels.FileChannel.open(Unknown","Source)","at","org.apache.lucene.store.MMapDirectory.openInput(MMapDirectory.java:238)","at","org.apache.lucene.store.NRTCachingDirectory.openInput(NRTCachingDirectory.java:181)","at","org.apache.lucene.codecs.compressing.CompressingStoredFieldsReader.<init>(CompressingStoredFieldsReader.java:150)","at","org.apache.lucene.codecs.compressing.CompressingStoredFieldsFormat.fieldsReader(CompressingStoredFieldsFormat.java:121)","at","org.apache.lucene.codecs.lucene50.Lucene50StoredFieldsFormat.fieldsReader(Lucene50StoredFieldsFormat.java:173)","at","org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:127)","...","21","more",",code=500}","","

HTTP","ERROR","500

","

Problem","accessing","/solr/emdb/select.","Reason:","

","{metadata={error-class=org.apache.solr.core.SolrCoreInitializationException,root-error-class=java.nio.file.NoSuchFileException},msg=SolrCore","'emdb'","is","not","available","due","to","init","failure:","Error","opening","new","searcher,trace=org.apache.solr.core.SolrCoreInitializationException:","SolrCore","'emdb'","is","not","available","due","to","init","failure:","Error","opening","new","searcher","at","org.apache.solr.core.CoreContainer.getCore(CoreContainer.java:1740)","at","org.apache.solr.servlet.HttpSolrCall.init(HttpSolrCall.java:253)","at","org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:538)","at","org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:419)","at","org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:351)","at","org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1602)","at","org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:540)","at","org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:146)","at","org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)","at","org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:257)","at","org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1711)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:255)","at","org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1347)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:203)","at","org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:480)","at","org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1678)","at","org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:201)","at","org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1249)","at","org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:144)","at","org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:220)","at","org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:152)","at","org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)","at","org.eclipse.jetty.rewrite.handler.RewriteHandler.handle(RewriteHandler.java:335)","at","org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)","at","org.eclipse.jetty.server.Server.handle(Server.java:505)","at","org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:370)","at","org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:267)","at","org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:305)","at","org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:103)","at","org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:117)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:333)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:310)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:168)","at","org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:126)","at","org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:366)","at","org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:781)","at","org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:917)","at","java.base/java.lang.Thread.run(Unknown","Source)","Caused","by:","org.apache.solr.common.SolrException:","Error","opening","new","searcher","at","org.apache.solr.core.SolrCore.<init>(SolrCore.java:1052)","at","org.apache.solr.core.SolrCore.<init>(SolrCore.java:881)","at","org.apache.solr.core.CoreContainer.createFromDescriptor(CoreContainer.java:1251)","at","org.apache.solr.core.CoreContainer.lambda$load$13(CoreContainer.java:765)","at","com.codahale.metrics.InstrumentedExecutorService$InstrumentedCallable.call(InstrumentedExecutorService.java:202)","at","java.base/java.util.concurrent.FutureTask.run(Unknown","Source)","at","org.apache.solr.common.util.ExecutorUtil$MDCAwareThreadPoolExecutor.lambda$execute$0(ExecutorUtil.java:210)","at","java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown","Source)","at","java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown","Source)","...","1","more","Caused","by:","org.apache.solr.common.SolrException:","Error","opening","new","searcher","at","org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:2162)","at","org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:2282)","at","org.apache.solr.core.SolrCore.initSearcher(SolrCore.java:1112)","at","org.apache.solr.core.SolrCore.<init>(SolrCore.java:993)","...","9","more","Caused","by:","org.apache.lucene.index.CorruptIndexException:","Problem","reading","index.","(resource=/var/solr/data/emdb/data/restore.20260811200813409/_90bku.fdt)","at","org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:144)","at","org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:84)","at","org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:177)","at","org.apache.lucene.index.ReadersAndUpdates.getReadOnlyClone(ReadersAndUpdates.java:219)","at","org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:109)","at","org.apache.lucene.index.IndexWriter.getReader(IndexWriter.java:526)","at","org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:116)","at","org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:92)","at","org.apache.solr.core.StandardIndexReaderFactory.newReader(StandardIndexReaderFactory.java:39)","at","org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:2126)","...","12","more","Caused","by:","java.nio.file.NoSuchFileException:","/var/solr/data/emdb/data/restore.20260811200813409/_90bku.fdt","at","java.base/sun.nio.fs.UnixException.translateToIOException(Unknown","Source)","at","java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown","Source)","at","java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown","Source)","at","java.base/sun.nio.fs.UnixFileSystemProvider.newFileChannel(Unknown","Source)","at","java.base/java.nio.channels.FileChannel.open(Unknown","Source)","at","java.base/java.nio.channels.FileChannel.open(Unknown","Source)","at","org.apache.lucene.store.MMapDirectory.openInput(MMapDirectory.java:238)","at","org.apache.lucene.store.NRTCachingDirectory.openInput(NRTCachingDirectory.java:181)","at","org.apache.lucene.codecs.compressing.CompressingStoredFieldsReader.<init>(CompressingStoredFieldsReader.java:150)","at","org.apache.lucene.codecs.compressing.CompressingStoredFieldsFormat.fieldsReader(CompressingStoredFieldsFormat.java:121)","at","org.apache.lucene.codecs.lucene50.Lucene50StoredFieldsFormat.fieldsReader(Lucene50StoredFieldsFormat.java:173)","at","org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:127)","...","21","more",",code=500}

","",""],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Kern DM","author_orcid":"0000-0001-8529-9045"},{"name":"Sorum B","author_orcid":"0000-0001-6742-1094"},{"name":"Hoel CM","author_orcid":"0000-0002-1344-0780"},{"name":"Sridharan S","author_orcid":null},{"name":"Remis JP","author_orcid":null},{"name":"Toso DB","author_orcid":null},{"name":"Brohawn SG","author_orcid":"0000-0001-6768-3406"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs","volume":null,"country":"","first_page":null,"last_page":null,"year":"2020","language":null,"doi":"10.1101/2020.06.17.156554","pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"3.2 TB","experiment_type":"EMDB","scale":null,"related_pdb_entries":["","414 Request-URI Too Large","","

414 Request-URI Too Large

","

nginx","",""],"entry_doi":"10.6019/EMPIAR-10612"}}