{"EMPIAR-11837":{"imagesets":[{"segmentations":[],"name":"Unaligned multi-frame micrographs of MERS 5' stem-loops 5 RNA.","directory":"data/MERS_SL5/exposures","category":"micrographs - multiframe","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":13244,"frames_per_image":40,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED 16 BIT INTEGER","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"data/MERS_SL5/exposures/GridSquare_*/*_Fractions.mrc","picked_particles_file_pattern":"","picked_particles_directory":"","details":"These micrographs were collected with a Titan Krios G3i, 300kV and a Falcon 4 detector. Over the collection, the sample was exposed evenly to 49.97 electrons per angstrom squared with a total exposure time of 4.74 seconds. Desired defocuses ranged from -1 to -2 nm. The exposures are gain corrected.","image_width":"4096","image_height":"4096"},{"segmentations":[],"name":"Extracted particles and orientations for final reconstruction of MERS 5' stem-loop 5 RNA.","directory":"data/MERS_SL5/particles","category":"picked particles - single frame - processed","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":286094,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":0.82,"pixel_height":0.82,"micrographs_file_pattern":"","picked_particles_file_pattern":"data/MERS_SL5/particles/data/*mrc","picked_particles_directory":"data/MERS_SL5/particles/data","details":"Particles extracted from motion-corrected micrographs. The orientations for the final reconstruction can be found in data/MERS/particles/conformation*.cs for all 3 conformations.","image_width":"360","image_height":"360"}],"workflow_file":null,"grant_references":[{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"R35GM122579","country":"United States"},{"funding_body":"Howard Hughes Medical Institute (HHMI)","code":"N/A","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)","code":"U24GM129541","country":"United States"},{"funding_body":"National Science Foundation (NSF, United States)","code":"GRFPDGE1656518","country":"United States"}],"version_history":[],"title":"Cryo-EM of MERS 5' proximal stem-loop 5","principal_investigator":[{"author_orcid":"0000-0002-8910-3078","middle_name":null,"organization":"Department of Bioengineering, James H. Clark Center, Stanford University; CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory","street":"318 CAMPUS DR","town_or_city":"Stanford","state_or_province":"CA","post_or_zip":"94305","telephone":null,"fax":null,"first_name":"Wah","last_name":"Chiu","email":"wahc [at] stanford.edu","country":"United States","entry":"EMPIAR-11837"}],"status":"REL","deposition_date":"2023-11-28","release_date":"2024-04-17","obsolete_date":null,"update_date":"2024-04-17","corresponding_author":{"author":{"author_orcid":"0000-0001-7497-0972","middle_name":null,"organization":"Department of Biochemistry, Stanford University; Howard Hughes Medical Institute","street":"279 Campus Dr W","town_or_city":"Stanford","state_or_province":"CA","post_or_zip":"94305","first_name":"Rhiju","last_name":"Das","country":"United States"}},"authors":[{"author":{"name":"Kretsch RC","author_orcid":"0000-0002-6935-518X"}},{"author":{"name":"Xu L","author_orcid":"0000-0002-1200-8937"}},{"author":{"name":"Zheludev IN","author_orcid":"0000-0002-9572-0574"}},{"author":{"name":"Zhou X","author_orcid":"0000-0002-0722-7334"}},{"author":{"name":"Huang R","author_orcid":"0009-0009-6136-8013"}},{"author":{"name":"Nye G","author_orcid":"0009-0001-6698-9988"}},{"author":{"name":"Li S","author_orcid":"0000-0002-7041-5960"}},{"author":{"name":"Zhang K","author_orcid":"0000-0003-0414-4776"}},{"author":{"name":"Chiu W","author_orcid":"0000-0002-8910-3078"}},{"author":{"name":"Das R","author_orcid":"0000-0001-7497-0972"}}],"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":"Kretsch RC","author_orcid":"0000-0002-6935-518X"},{"name":"Xu L","author_orcid":"0000-0002-1200-8937"},{"name":"Zheludev IN","author_orcid":"0000-0002-9572-0574"},{"name":"Zhou X","author_orcid":"0000-0002-0722-7334"},{"name":"Huang R","author_orcid":"0009-0009-6136-8013"},{"name":"Nye G","author_orcid":"0009-0001-6698-9988"},{"name":"Li S","author_orcid":"0000-0002-7041-5960"},{"name":"Zhang K","author_orcid":"0000-0003-0414-4776"},{"name":"Chiu W","author_orcid":"0000-0002-8910-3078"},{"name":"Das R","author_orcid":"0000-0001-7497-0972"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses","volume":"121","country":"","first_page":null,"last_page":null,"year":"2024","language":"English","doi":"10.1073/pnas.2320493121","pubmedid":"38427602","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Proceedings of the National Academy of Sciences of the United States of America","journal_abbreviation":"Proc Natl Acad Sci U S A","issue":"10","preprint":false},{"authors":[{"name":"Kretsch RC","author_orcid":null},{"name":"Xu L","author_orcid":"0000-0002-1200-8937"},{"name":"Zheludev IN","author_orcid":"0000-0002-9572-0574"},{"name":"Zhou X","author_orcid":"0000-0002-0722-7334"},{"name":"Huang R","author_orcid":null},{"name":"Nye G","author_orcid":null},{"name":"Li S","author_orcid":"0000-0002-7041-5960"},{"name":"Zhang K","author_orcid":null},{"name":"Chiu W","author_orcid":null},{"name":"Das R","author_orcid":"0000-0001-7497-0972"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"Tertiary folds of the SL5 RNA from the 5′ proximal region of SARS-CoV-2 and related coronaviruses","volume":null,"country":"","first_page":null,"last_page":null,"year":"2023","language":null,"doi":"10.1101/2023.11.22.567964","pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"16.7 TB","experiment_type":"EMDB","scale":"molecule","related_pdb_entries":["","414 Request-URI Too Large","","

414 Request-URI Too Large

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