{"EMPIAR-12390":{"imagesets":[{"segmentations":[],"name":"Raw micrographs of deposited and revitrified T20S proteasome","directory":"data","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":3641,"frames_per_image":50,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"","image_width":"5760","image_height":"4092"}],"workflow_file":null,"grant_references":[{"funding_body":"Swiss National Science Foundation","code":"TMCG-2_213773","country":"Switzerland"}],"version_history":[],"title":"Single Particle cryo-EM dataset of the deposited and revitrified T20S proteasome","principal_investigator":[{"author_orcid":"0000-0002-8869-5999","middle_name":null,"organization":"Laboratory of Molecular Nanodynamics, Institute for Chemical Sciences and Engineering, Ecole Polytechnique Federale Lausanne","street":null,"town_or_city":"Lausanne","state_or_province":null,"post_or_zip":"CH-1015","telephone":null,"fax":null,"first_name":"Ulrich","last_name":"Lorenz","email":"ulrich.lorenz [at] epfl.ch","country":"Switzerland","entry":"EMPIAR-12390"}],"status":"REL","deposition_date":"2024-11-04","release_date":"2025-07-25","obsolete_date":null,"update_date":"2025-09-22","corresponding_author":{"author":{"author_orcid":"0000-0002-7721-5048","middle_name":"Sarah","organization":"Laboratory of Molecular Nanodynamics, Institute for Chemical Sciences and Engineering, Ecole Polytechnique Federale Lausanne","street":null,"town_or_city":"Lausanne","state_or_province":null,"post_or_zip":"CH -1015","first_name":"Monique","last_name":"Straub","country":"Switzerland"}},"authors":[{"author":{"name":"Straub MS","author_orcid":"0000-0002-7721-5048"}},{"author":{"name":"Harder OF","author_orcid":"0000-0002-5742-9217"}},{"author":{"name":"Mowry NJ","author_orcid":"0000-0001-8635-7075"}},{"author":{"name":"Barrass SV","author_orcid":"0000-0001-7319-6268"}},{"author":{"name":"Hruby J","author_orcid":"0000-0002-5837-9119"}},{"author":{"name":"Drabbels M","author_orcid":"0000-0001-8611-2684"}},{"author":{"name":"Lorenz UJ","author_orcid":"0000-0002-8869-5999"}}],"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":"Straub MS","author_orcid":"0000-0002-7721-5048"},{"name":"Harder OF","author_orcid":"0000-0002-5742-9217"},{"name":"Mowry NJ","author_orcid":"0000-0001-8635-7075"},{"name":"Barrass SV","author_orcid":"0000-0001-7319-6268"},{"name":"Hruby J","author_orcid":"0000-0002-5837-9119"},{"name":"Drabbels M","author_orcid":"0000-0001-8611-2684"},{"name":"Lorenz UJ","author_orcid":"0000-0002-8869-5999"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Laser flash melting cryo-EM samples to overcome preferred orientation","volume":"22","country":"","first_page":"1880","last_page":"1886","year":"2025","language":"English","doi":"10.1038/s41592-025-02796-y","pubmedid":"40877464","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature methods","journal_abbreviation":"Nat Methods","issue":"9","preprint":false}],"dataset_size":"555.0 GB","experiment_type":"EMDB","scale":"molecule","related_pdb_entries":["","414 Request-URI Too Large","","

414 Request-URI Too Large

","

nginx","",""],"entry_doi":"10.6019/EMPIAR-12390"}}