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FAQ (15)

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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.

See following items for the details.

Related info.:Q: How do you make the movies in EM Navigator? / Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.? / Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?

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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?

External links:The release schedule of PDB data, the available data at each wwPDB site

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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)

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Q: Where is the official data of EMDB?

A: Following three are the official, have the same contents, and update at same time

CountryOrganizationHTTP URLFTP URL
JapanPDBjhttps://ftp.pdbj.org/pub/emdbftp://ftp.pdbj.org/pub/emdb
UKEBI PDBehttps://ftp.ebi.ac.uk/pub/databases/emdbftp://ftp.ebi.ac.uk/pub/databases/emdb
USAwwPDB & RCSB PDBhttps://ftp.wwpdb.org/pub/emdbftp://ftp.wwpdb.org/pub/emdb

Related info.:Q: When the data are updated?

External links:About the contents of the PDBj data site - PDBj

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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? / EMDB map data format

External links:Kimura et al. Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature 389, 206, 1997 doi:10.1038/38323

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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.

Related info.:Q: Is an EM map electron-density map? / Q: Which software is suitable to view EMDB maps? / EMDB map data format

External links:EMDB Map Distribution Format Description (PDF document) / CCP4 map format

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Q: Which software is suitable to view EMDB maps?

A: Many software packages can display CCP4 map data

Related info.:Q: What is the format for the maps? / Q: How do you make the movies in EM Navigator? / EMDB map data format

External links:UCSF Chimera Home Page

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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

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Q: What are the data sources of EM Navigator?

A: EMDB and PDB electron microscopy dat

  • 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

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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

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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 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

Related info.:Q: Which software is suitable to view EMDB maps? / Q: How do you make the images for the structure data? What do their colors mean? / Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.? / Movie viewer / "Movies out of date"

External links:UCSF Chimera Home Page / Jmol: an open-source Java viewer for chemical structures in 3D / FFmpeg

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Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.?

A: in semi-automatic process with UCSF Chimera

  • Method:
    • We make been creating the images and movies for structure entries in EM Navigator using UCSF Chimera in semi-automatic process.
  • Orientation:
    • The structures are manually rotated to be seen in "good" orientation (usually, figures of the paper is refererd), or in similar orientation with similar structure data.
    • For the case of icosahedral symmetry structure data, they are viewed normal to their five-fold axis, while typical view of such the structure data are along the two-fold or three-fold axes. This is to unify the orientation with structure data with pseudo-icosahedral symmetry, such as bacteriophage with tail structures.
  • Color:
    • In EM Navigator, multiple images are made for a single entry. In Omokage search, image of "colored surface view" are shown.
    • The surface are colored by height, distance, or cylindrical radius. See the detail page for the coloring of particular images.

Related info.:Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.? / Q: How do you make the movies in EM Navigator? / Q: How do you make the images for the structure data? What do their colors mean?

External links:UCSF Chimera Home Page

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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

  • Orientation:
    • 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.
  • Color:
    • 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.
  • Problems:
    • 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 of EMDB entries in Yorodumi, Omokage, etc.?

External links:Jmol: an open-source Java viewer for chemical structures in 3D

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Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?

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

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Related info.:PDBj / Yorodumi annotation

External links:Contact to PDBj / Protein Data Bank Japan at IPR, Osaka-univ.

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Q: What is difference in PDB coordinate formats?

A: As follows

FormatmmCIF compatibleFormat based onProviderComment
PDBx/mmCIF-CIF > STAR > plain textwwPDBOfficail data format
PDBnoplain textwwPDBLegacy officail
PDBMLyesXML > plain textwwPDBFor programers & develpers
PDBx/mmJSONyesJSON > plain textPDBjFor programers & develpers

Related info.:PDBx/mmCIF format / PDB format / PDBx/mmJSON format

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