-Search & filter documents
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.:Omokage search
+Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.
+Dec 4, 2015. The article about Omokage search is published online
The article about Omokage search is published online
- Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Suzuki Hirofumi, Kawabata Takeshi, and Nakamura Haruki, Bioinformatics. (2015) btv614
main text (HTML, Open Access), supplementray data (PDF, Open Access)
Related info.:Omokage search / gmfit
+Nov 28, 2015. Omokage search starts to support SASBDB models
Omokage search starts to support SASBDB models
- Models data in SASBDB are added to the Omokage search database.
- SASBDB is a databank for small angle scattering data
- A SASBDB model can be used as a search query.
- The search result may include SASBDB models.
Related info.:Omokage search / SASBDB / Comparison of 3 databanks
+Dec 10, 2014. PDB "SPLIT" entries are replaced with "LARGE" entries
PDB "SPLIT" entries are replaced with "LARGE" entries
- Structure data deposited as multiple PDB entries are replace with single combined entries, which were previously stored as "large structure". See here for details.
- In EM Navigator, many ribosome and several virus entries are replaced.
+Sep 22, 2014. New service: Omokage search
New service: Omokage search
Related info.:Omokage search
+Mar 30, 2013. New page of in EM Navigator, statistics
New page of in EM Navigator, statistics
Related info.:EMN Statistics
+Jan 16, 2013. New EMDB header format
New EMDB header format
- Format of the EMDB header file (XML based meta data file, not the map data themselves) are updated to version 1.9 (see here for details)
- Now, the contents of EM Navigator are based on the new data. Colors of some parts (e.g. bars in top area of the Detail pages) indicate 3D-reconstruction method, instead of 'aggregation states'.
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.:Changes in new EM Navigator and Yorodumi
+Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links:The 2017 Nobel Prize in Chemistry - Press Release
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Feb 20, 2018. PDBj/BINDS workshop in Osaka University
PDBj/BINDS workshop in Osaka University
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jul 5, 2019. Downlodablable text data
+Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?
A: Hirofumi Suzuki (PDBj / IPR, Osaka University)
- hirofumi protein.osaka-u.ac.jp
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Facebook -
Related info.:PDBj / Yorodumi annotation
+Q: What is the data source of EM Navigator?
A: EMDB and PDB electron microscopy data
- Main source:
- all EMDB entries
- PDB entries with method information (exptl.details) including "electron microscopy" or "electron diffraction"
- Some contents and infromation are original of EM Navigator:
- Movies and their snapshot images
- Projection and slice images
- Some information about related data and similar structures.
Related info.:EM Navigator / EMDB / PDB / EMN Search / EMN Papers / EMN Statistics
+Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations?
A: Yes, plese. The EM Navigator movies and their snapshots are open to public. It would be appreciated if you would cite it as "EM Navigator, PDBj".
Related info.:Movie viewer
External links:Terms and conditions - PDBj
+Q: Is 3DEM same as electron cryo microscopy (cryoEM)?
A: No, "3DEM" and "cryoEM" are distinct to be exact.
- However, they are closely related. Some people call 3DEM "cryoEM
- Many but not all the 3DEM analyses are perfomed with cryoEM. In EMDB and PDB, there are some entries, whose structure data were obtained in non-cryo contition.
Related info.:3D electron microscopy (3DEM) / electron cryo microscopy (cryoEM)
+Q: How do you make the images for the structure data? What do their colors mean?
A: Images of EMDB entries are made for EM Navigator, and ones of PDB entries are for Yorodumi. There are several patterns of coloring.
Related info.:Q: How do you make the movies in EM Navigator? / Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?
+Q: Where is the official data of EMDB?
A: Following three are the official, have the same contents, and update at same time
Country Organization URL Japan PDBj ftp://ftp.pdbj.org/pub/emdb UK EBI ftp://ftp.ebi.ac.uk/pub/databases/emdb USA wwPDB ftp://ftp.wwpdb.org/pub/emdb
Related info.:Q: When the data are updated?
+Q: How do you make the movies in EM Navigator?
A: Series of images are recorded by UCSF-Chimera or Jmol. Then, they are encoded into movie files by avconv command in the libav package.
- This is an example of Chimera script.
system mkdir img1 movie reset movie record fformat png directory ./img1/ pattern img* roll y 2 180; wait wait 15 roll x 2 180; wait reset pos1; wait reset pos2 180; wait reset pos1 180; wait reset movie stop("pos1" and "pos2" are saved position, which are the start and end of sectioning motion)
- Chimera session files distributed with the movie files may be helpfull.
Related info.:Q: How do you make the images for the structure data? What do their colors mean? / Movie viewer / "Movies out of date"
+Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?
A: We are making them by full-automatic process using Jmol. Their styles are depend on the data type
- Icosahedral assembly: Original orientation.
- Helical assembly: 6 orientation (+/- of X, Y, Z direction) images are generated in jpeg format. Then, the largest file is chosen. (large JPEG => many dots/colors)
- Others: by "rotate best" command of Jmol.
- Ribosomes: by "rotate best" command of Jmol. Only RNA coordinates are used for the orientation.
- monomer AUs: by N->C (blue->red) rainbow
- BUs of monomer AUs: by "color molecule" (Jmol's coloring)
- multimer AUs and thier BUs (including monomer BUs): by "color chain". For this coloring, Jmol uses not a rainbow color but the colors determined by the chain-ID.
- BU models are generated by Jmol's system. It works well for the most data, but there are some exception.
- Checking and fixing processes of the many (>200,000) images are in progress. There are still some wrong images.
Related info.:Q: How do you make the images for the structure data? What do their colors mean?
+Q: What is the format for the maps?
A: It is CCP4 map format
- It's binary data with header for map geometry and body for density values.
- Here is description of EMDB map data. EMDB_map_Format.pdf
Related info.:Q: Is an EM map electron-density map? / Q: Which software is suitable to view EMDB maps?
External links:CCP4 map format
+Q: Is an EM map electron-density map?
A: No. But, they are very similar.
- To be exact, 3D map derived by 3D-EM is related to Coulomb potential (or electron potential), rather than electron density.
- The difference seems to be ignored in the most studies of atomic model building and fitting.
- Thers are some reports that protonation state affects the density. (see the ext. link)
Related info.:Q: What is the format for the maps?
+Q: Which software is suitable to view EMDB maps?
A: Many software packages can display CCP4 map data.
- Some softwares introduced in this page shoud be suitable.
Software Tools For Molecular Microscopy/Visualization and modeling tools - Wikibooks
- Movies for EMDB map data in the EM Navigator are made by UCSF-Chimera.
- UCSF-Chimera seems to be the major software in the community.
Related info.:Q: What is the format for the maps?
External links:UCSF Chimera Home Page
+Q: What is "EMD"?
A: EMD (or emd) is "prefix" for ID number of EMDB
- At the beginning, the EMDB was also called EMD.
- Since the EM Navigator uses PDB and EMDB data, ID codes are indicated as [database name]-[ID], without the prefix. e.g. EMDB-1001, PDB-1brd
Related info.:EMDB / EM Navigator / Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page) / ID/Accession-code notation in Yorodumi/EM Navigator
+Q: When the data are updated?
A: EMDB and PDB entries are released/updated every Wednesday at 0:00GMT/9:00JST
- Data in EM Navigator, Yorodumi, and Omokage are updated at the same time.
- SASBDB seems to update irregularly.
Related info.:Q: Where is the official data of EMDB?
+Comparison of 3 databanks
|method||main data||str. data format||meta data format|
|PDB||various||atomic model||PDBx/mmCIF, etc.||PDBx/mmCIF, etc.|
|EMDB||3DEM||3D map||CCP4 map||EMDB XML|
|SASBDB||Small Angle Scattering (SAS)||SAS profile (+/- 3D models)||PDB + sasCIF||ASCII + sasCIF|
Related info.:EMDB / PDB / SASBDB / Covid-19 info / ID/Accession-code notation in Yorodumi/EM Navigator / Experimental methods, equipments, and software data
+3D electron microscopy (3DEM)
A generic term of electron microscopic analyses to obtain 3D structures
- Analyses such as electron tomography, single particle analysis, and electron diffraction are included.
Aggregation states Methods generally used "individual structure" electron tomography "single particle" single particle analysis "icosahedral" single particle analysis "helical" helical reconstruction / single particle analysis "2D/3D-crystal" electron diffraction / Fourier filtering
- Characteristics compared to X-ray crystallography and NMR:
- Advantage: Wider applicability of sample (not require high-purity or high-concentration smaple, and useful for more huge, complex, flexible, and less uniform sample)
- Disadvantage (previous): Lower resolution (hard to get atomic-level resolution data)
- Disadvantage (new): High-performance electron microscopes and their maintenance costs are quite expensive.
Related info.:EMDB / electron cryo microscopy (cryoEM)
Page for Covid-19 featured contents.
Related info.:Comparison of 3 databanks / Aug 12, 2020. New: Covid-19 info
Documentation for Yorodumi, EM Navigator, Omokage, etc.
3D electron microscopy data browser
- Browser for 3D electron microscopy (3D-EM) data of biological molecules and assemblies.
Related info.:EMDB / PDB / PDBj / Q: What is the data source of EM Navigator? / EMN Search / EMN Papers / EMN Gallery / EMN Statistics / Changes in new EM Navigator and Yorodumi
Database of articles cited by 3DEM data entries
- Database of articles cited by 3DEM data entries in EMDB and PDB
- Using PubMed data
Related info.:EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi
3DEM data search
- Advanced data search for EMDB and EM data in PDB widh various search and display options
Related info.:EMDB / PDB / EM Navigator / Q: What is the data source of EM Navigator? / Yorodumi Search / Jul 5, 2019. Downlodablable text data
Function & Homology similarity search
- Based on the similarity of Function & Homolog items related to the structure data, similar data are searched from structure databases.
Related info.:Function and homology information
Image gallery of 3DEM data
- Categorization is done by EM Navigator manager manually. It is not strict.
Related info.:EMDB / PDB / EM Navigator
Search structure by SHAPE
- "Omokage search" is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.
- The search is performed ageinst >200,000 structure data, which consists of EMDB map data, PDB coordinates (deposited units (asymmetric units, usually), PDB biological units, and SASBDB mdoels).
- For the search query, you can use either a data in the PDB/EMDB/SASBDB or your original model.
- Supported formats are PDB (atomic model, SAXS bead model, etc.) and CCP4/MRC map (3D density map).
- Shape comparison is performed by iDR profile method, which uses 1D-distance profiles of super-simplified models generated by vector quantizaion in Situs package.
Related info.:Comparison of 3 databanks / Sep 22, 2014. New service: Omokage search / gmfit / Re-ranking by gmfit
Database of articles cited by EMDB/PDB/SASBDB data
- Database of articles cited by EMDB, PDB, and SASBDB entries
- Using PubMed data
Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi
Statistics of 3DEM data in table and graph styles
- The table can be sorted. Click the column header to be sorted. (second click to reverse, [Shift]+click for multi-column sort)
- To show the bar graph in table mode, point the column/row header by mouse courser.
- To search the correspoinding data, click the cell of value.
Related info.:EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Mar 30, 2013. New page of in EM Navigator, statistics
Taxonomy data in EMDB/PDB/SASBDB
- Taxonomy database of sample sources of data in EMDB/PDB/SASBDB
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Mar 5, 2020. Novel coronavirus structure data
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi
Cross-search of EMDB, PDB, SASBDB, etc.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / EMN Search / Yorodumi / Experimental methods, equipments, and software data / Function and homology information / Changes in new EM Navigator and Yorodumi
+electron cryo microscopy (cryoEM)
Electron microscopy where the sample is studied at cryogenic temperatures
Related info.:3D electron microscopy (3DEM) / Q: Is 3DEM same as electron cryo microscopy (cryoEM)?
External links:Cryo-electron microscopy - Wikipedia
Electron Microscopy Data Bank, Databank for 3DEM
Related info.:3D electron microscopy (3DEM) / Comparison of 3 databanks
+Function and homology information
Molecular function, domain, and homology information from related databases.
|Category||Name of database or definition|
|Function||Gene ontology, Enzyme Commission number, Reactome, etc.|
|Domain/homology||CATH, InterPro, SMART, etc.|
|Component||UniProt, GenBank, PDB chemical component, etc.|
Related info.:Information from PDBMLplus / Yorodumi Search / Yorodumi / F&H Search
a program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)
- Developed by Takeshi Kawabata in IPR, Osaka-univ.
- Used from Omokage search.
Related info.:Omokage search / Dec 4, 2015. The article about Omokage search is published online / Re-ranking by gmfit
External links:Pairwise gmfit
+Re-ranking by gmfit
The similarity ranking by Omokage search can be re-ordered according to correlation coefficient by gmfit, expecting incorporation of the (potential) benefits of two methods with following properties.
Method Speed Potential accuracy Omokage search
(iDR profile comparison)
(sub-msec / 1 comparison)
(1D profile comparison)
(Gaussian mixture model fitting)
(sub-sec / 1 comparison)
(comparison in 3D space)
Related info.:gmfit / Omokage search
+ID/Accession-code notation in Yorodumi/EM Navigator
|EMDB||EMDB-XXXX||EMDB-1001||prefix EMD- omitted|
|SASBDB||-||SASDA24||as it is|
Related info.:Comparison of 3 databanks / Q: What is "EMD"? / Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
An open-source viewer for chemical structures in 3D
|X-Y rotation||X-Y move||Zoom in/out|
|Mouse||left drag||[Ctrl] + right drag||center drag (vertical) / wheel|
|Touch||single finger||double finger||pinch|
Related info.:Molmil / Yorodumi
+Experimental methods, equipments, and software data
Database of experimental methods of EMDB, PDB and SABDB.
Related info.:Comparison of 3 databanks / Yorodumi Search
+Information from PDBMLplus
PDBMLplus is the XML format file including additional information relating to individual proteins. Currently, PDB files are lacking a detailed description of function, experimental conditions, and the like. And then such information was included to extended XML database, named PDBMLplus.
Related info.:PDBj / Function and homology information
WebGL based molecular viewer
- Mouse/touch operation
X-Y rotation X-Y move Zoom in/out Mouse left drag center drag / shift + left drag right drag / wheel Function menu: top left buttons on viewer screen Touch single finger pinch
Related info.:Jmol/JSmol / SurfView / Changes in new EM Navigator and Yorodumi
Visualization of 3DEM structure data by movies.
- Horizontal- and vertical- rotation motions and "slicing" motion are recorded in the movies.
- As the movie frame can be controlled by mouse/touch position, it can be operated interactively as a molecular viewer. According to the mouse/finger position and orientation of the motion on the movie panel, the model rotates on horizontal or vertical direction. By horizontal mouse/finger movement on the top part of the movie, the slicing motion is shown.
Related info.:Q: How do you make the movies in EM Navigator? / Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations? / SurfView / Changes in new EM Navigator and Yorodumi
+Changes in new EM Navigator and Yorodumi
Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)
- New user interface unified in EM Navigator, Yorodumi & Omokage search, supporting mobile devices as well as PCs.
- New Yorodumi replace the individual data page ("Detail page" of EM Navigator in the legacy system). It is unified browser for EMDB, PDB, and SASBDB entries integrated with EM Navigator and Omokage search.
- The viewers (structure/movie viewers) appear in pop-up windows. On a PC, multiple viewer windows can be opened. On mobile devices, the viewers support touch operation.
- New features:
- Molmil, molecular structure viewer, and SurfView, surface model viewer for EMDB map data, are available to view the 3D structures. Both viewers support mobile device use.
- Yorodumi support SASBDB entries.
- Some new pages such as Yorodumi Papers, citation database of structure data entries and Yorodumi Search, cross search by keywords
Related info.:EM Navigator / Yorodumi / SurfView / Molmil / Movie viewer / EMN Papers / Yorodumi Papers / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi
+"Movies out of date"
Movies with this annotation may not be up-to-date.
Related info.:Q: How do you make the movies in EM Navigator?
Protein Data Bank - The single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
Related info.:PDBj / Comparison of 3 databanks
External links:World Wide PDB
Protein Data Bank Japan.
Related info.:PDB / Information from PDBMLplus
Polysaccaride/carbohydrate data representation in PDB
- In July 2020, representation for polysaccaride/carbohydrate information in PDB is improved.
- The polysaccaride figures are generated by GlycanBuilder2. (Article)
- See following external links for other details.
Small Angle Scattering Biological Data Bank - Curated repository for small angle scattering data and models
- Develop & manage: BioSAXS group in EMBL
- Since 2014
Related info.:Comparison of 3 databanks
EMDB map surface models viewer on Web browsers
- The surface models shwon in this viewer are modified for simplification and data size reduction. To get views of full-resolution data, see movies instead.
- Mouse/touch operation
X-Y rotation X-Y move Zoom in/out Mouse left drag right drag center drag / wheel Touch single finger double finger pinch
Related info.:Movie viewer / Molmil / Changes in new EM Navigator and Yorodumi
Annotation by Yorodumi/EM Navigator manager
Related info.:Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?
-About Yorodumi Docs
Documentation for Yorodumi, EM Navigator, Omokage, etc.