-Search & filter documents
+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: 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?
+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: Where is the official data of EMDB?
A: Following three are the official, have the same contents, and update at same time
- Japan: ftp://ftp.pdbj.org/pub/emdb
- UK: ftp://ftp.ebi.ac.uk/pub/databases/emdb
- USA: ftp://ftp.wwpdb.org/pub/emdb
Related info.: Q: When the data are updated?
+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: 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: 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
+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: 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?
External links: Jmol: an open-source Java viewer for chemical structures in 3D
+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
-About Yorodumi Docs
Documentation for Yorodumi, EM Navigator, Omokage, etc.