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FAQ (13)

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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 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?

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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

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

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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?

    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.
    • 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

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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?

    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

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    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

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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 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"

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

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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 for the structure data? What do their colors mean?

    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)

    • 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

    External links: Haruki Nakamura Lab., Institute of Protein Research,Osaka University

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