3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
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This page is a legacy version and will be discarded in future. The new page is here.

EM Navigator is...
  • web site to browse 3D electron microscopy (3D-EM) data of biological molecules and assemblies,
  • based on EMDB and PDB data, (statistics)
  • for non-specialists, beginners, and experts in 3D-EM or structural/molecular biology,
  • run by PDBj.
  • FAQ

    3D-EM & Databases

    Q: What is the difference between PDB and EMDB?

    A: EMDB is for 3D maps by 3D-EM, while PDB is for atomic models.

  • Different points:
    Main data3D density mapsAtomic coordinates
    Experimental methods3D-EMOther than pure theoretical methods
  • Similar points:
  • main data of 3D structures of biological molecules, assemblies, or tissues
  • with rich meta-data (publication, expriment, sample, etc.)
  • open to public
  • Some data are depsitted on both of them.
  • Glossary: 3D electron microscopy

    Q: Is 3D-EM same as electron cryo microscopy (cryo-EM)?

    A: No, "3D-EM" and "cryo-EM" are distinct to be exact.

  • But, they are closely related. Some people call 3D-EM "cryo-EM".
  • Many but not all the 3D-EM analyses are perfomed with cryo-EM.
  • Glossary: 3D electron microscopy Glossary: electron cryo microscopy Cryo-electron microscopy - Wikipedia

    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
  • About EMDB map data

    Q: Tell me FTP server URL.

    Q: Are EM maps same as electron density maps?

    A: Approximately, yes.

  • To be exact, 3D map derived by 3D-EM is related to Coulomb potential, rather than electron density.
  • Q: What is the format for the maps?

    A: It is CCP4 map format

  • Here is description of EMDB map data: EMDB_map_Format.pdf
  • Q: Which software should I use to view the maps?

    A: 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.
  • About EM Navigator

    Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations?

    A: Yes, you can. The EM Navigator movies and their snapshots are open to public. It would be appreciated if you would cite it as "EM Navigator, PDBj".

    Terms of use of PDBj

    Q: How do you make the movies?

    A: Series of images are recorded by UCSF-Chimera or Jmol. Then, they are encoded into movies by FFmpeg

  • 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
    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.
  • Q: Who make these documents, web pages and movies in the EM Navigator?

    A: Hirofumi Suzuki (PDBj / IPR, Osaka University) makes.

    Further description will be added.

  • FAQs page at PDBj
  • FAQ page at EMDataBank.org
  • Glossary

    3D electron microscopy (3D-EM)

    A generic term of electron microscopic analyses to obtain 3D structurres

  • Analyses such as electron tomography, single particle analysis, and electron diffraction are included.
    Aggregation statesMethods generally used
    "individual structure"electron tomography
    "single particle"single particle analysis
    "icosahedral"single particle analysis
    "helical"helical reconstruction / single particle analysis
    "2D-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: Lower resolution (hard to get atomic-level resolution data)
  • electron cryo microscopy (cryo-EM)

    Electron microscopy where the sample is studied at cryogenic temperatures.

    Cryo-electron microscopy - Wikipedia

    EMDB: Electron Microscopy Data Bank

    Data bank for 3D-EM

  • EMDataBank.org
  • "Movies out of date"

    Movies with this annotation may not be up-to-date.

    EMDB map data are sometimes remediated. Unfortunately, the process of making movies in the EM Navigaotr are not fully automated, and it is very hard to remake the all to catch up. So, some movies and movie parameters are based on the older data, and may be improper for new map data.

  • 2017-11-15: Latest structures

    Other latests: New EMDB meta data, Updated EMDBs, Updated PDBs
  • 2017-11-08: Latest structures
  • 2017-11-01: Latest structures
  • 2017-10-25: Latest structures
  • 2017-10-18: Latest structures
  • 2017-10-11: Latest structures
  • 2017-10-04: Latest structures
  • 2017-09-27: Latest structures
  • 2017-09-20: Latest structures
  • 2017-09-13: Latest structures
  • 2016-08-31: New EM Navigator & Yorodumi
    On 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions. See this page for details. News, Aug 31, 2016 - Yorodumi Docs
  • 2015-12-12: New EM Navigator will come.
    We have been developing the new EM Navigator.You can try the test version.
  • 2014-12-10: 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.
  • 2014-09-22: New service: A shape similarity search service, "Omokage search" is started.
  • 2013-03-30: New page, statistics
    Resolution vs. Method, Specimen Temperature vs. Resolution, etc. may be interesting.
  • 2013-01-16: 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'.
  • 2012-07-23: New player and format for movies
    The movie player embedded on pages is changed to jPlayer, which is a media tool using HTML5/Flash solutions and supporting various platforms including iOS and Androird. Now, distributed movies are in H.264/MPEG-4 AVC(.mp4) and WebM/VP8 (.webm) formats.
  • 2012-04-13: Distribution of movie files in "asf" and "mov" format is resumed.
  • 2012-03-07: URL of EMDB FTP server was changed
    For join of EMDB data to PDB archive, the URL of the Japanese FTP server to download EMDB data was changed.
    New URL: ftp://pdb.protein.osaka-u.ac.jp/pub/emdb
    (Use in web browsing has no change.)
  • 2012-02-03: Currently, movie files in "asf" and "mov" format are unavailable.
  • 2011-08-15: PDB strucutre viewers replaced by movies. Now, all the EM structures of both PDB and EMDB are displayed in movies. (Please, use Yorodumi for interactive visualization)
  • 2010-08-27: Movie interface in Detail page is improved
  • 2010-07-15: Many EMDB map data are remediated. See this page for details. Currently, some movies and related data in EM Navigator are improper for the remediated data.
  • 2010-07-13: New page: Document page.
  • 2010-07-13: New page: Diagram page (beta).
  • 2010-07-02: Table page is integrated with improved List page
  • PDBj news
  • Omokage project

    Omokage (Overall morphology comparing system for EM data)

  • Omokage is structure comparison system using vector quantization.
  • It calculates similarities of the overall shapes, rather than detailed structures.
  • It is not accurate comparison.
  • The documentatin is under construction.
  • It is beta (under testing).
  • List of similar structures

  • The lists are sorted by Omokage scores.
  • Diagram page (Omokage map)

  • The diagram is indicating the relationships of the structure similarities.
  • It is generated by multidimensional scaling of Omokage scores.
  • The green boxes indicates EMDB data, and the blue boxes are PDB data. The image and title are appeared when a boxe is clicked.
  • The diagram can be moved by mouse dragging, and zoomed in/out by the "zoom" slider.
  • When you input a EMDB/PDB ID code in the "ID" box, the corresponding data will be focused.
  • When you input words in the "Keywords" box, the data related to the keywords are colored.