3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
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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:
    EMDBPDB
    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_mapFormat_v1.0.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
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.

    • 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