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EM Navigator3D-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.
| EMDB | PDB | |
|---|---|---|
| Main data | 3D density maps | Atomic coordinates |
| Experimental methods | 3D-EM | Other than pure theoretical methods |
Q: Is 3D-EM same as electron cryo microscopy (cryo-EM)?
A: No, "3D-EM" and "cryo-EM" are distinct to be exact.
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
About EMDB map data
Q: Tell me FTP server URL.
A: FTP sites are as follows.
Q: Are EM maps same as electron density maps?
A: Approximately, yes.
Q: What is the format for the maps?
A: It is CCP4 map format
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
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 PDBjQ: 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
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)
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.
3D electron microscopy (3D-EM)
A generic term of electron microscopic analyses to obtain 3D structurres
| 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-crystal" | electron diffraction / Fourier filtering |
electron cryo microscopy (cryo-EM)
Electron microscopy where the sample is studied at cryogenic temperatures.
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.
Other latests: New EMDB meta data, Updated EMDBs, Updated PDBs
statisticsResolution vs. Method, Specimen Temperature vs. Resolution, etc. may be interesting.
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'.
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.
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.)
Yorodumi for interactive visualization)e.g.
EMDB sites
PDB sites
PDBj: Protein Data Bank Japan
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