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News (6)

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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FAQ (2)

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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: 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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    Information (11)

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    Yorodumi (legacy version)

    Touch the mechanism of life

    URL: https://pdbj.org/emnavi/viewtop.php?lgc=1

      Related info.: EMDB / PDB / Yorodumi / Aug 31, 2016. New EM Navigator & Yorodumi / Changes in new EM Navigator and Yorodumi

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      Yorodumi

      Thousand views of thousand structures

      URL: https://pdbj.org/emnavi/quick.php

      • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
      • All the functionalities will be ported from the levgacy version.
      • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

      Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

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      Yorodumi Search

      Cross-search of EMDB, PDB, SASBDB, etc.

      URL: https://pdbj.org/emnavi/ysearch.php

        Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / EMN Search / Yorodumi / Changes in new EM Navigator and Yorodumi

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        Yorodumi Papers

        Database of articles cited by EMDB/PDB/SASBDB data

        URL: https://pdbj.org/emnavi/pap.php

        • Database of articles cited by EMDB, PDB, and SASBDB entries
        • Using PubMed data

        Related info.: EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

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        Yorodumi Speices

        Taxonomy data in EMDB/PDB/SASBDB

        URL: https://pdbj.org/emnavi/taxo.php

        • Taxonomy database of sample sources of data in EMDB/PDB/SASBDB

        Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks

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        Yorodumi Docs

        Documentation for Yorodumi, EM Navigator, Omokage, etc.

        URL: https://pdbj.org/emnavi/doc.php

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          Jmol/JSmol

          An open-source viewer for chemical structures in 3D

        • Mouse/touch operation
          X-Y rotationX-Y moveZoom in/out
          Mouseleft drag[Ctrl] + right dragcenter drag (vertical) / wheel
          Touchsingle fingerdouble fingerpinch
          Jmol menu: [Ctrl] + click / right click
        • Related info.: Molmil / Yorodumi

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

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          Molmil

          WebGL based molecular viewer

          • Molmil runs on Web browser on a smartphone or tablet device as well as PC. (Molmil is based on WebGL and Javascript).
          • Mouse/touch operation
            X-Y rotationX-Y moveZoom in/out
            Mouseleft dragcenter drag / shift + left dragright drag / wheelFunction menu: top left buttons on viewer screen
            Touchsingle fingerpinch
          • Currently, functionalities about integration with Yorodumi page is quite limited. In the new Yorodumi, Molmil will succeed to all the functionalities of Jmol in legacy Yorodumi.

          Related info.: Jmol/JSmol / SurfView / Changes in new EM Navigator and Yorodumi

          External links: Documentation of Molmil in PDBj site / Molmil's page in GitHub

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          Changes in new EM Navigator and Yorodumi

          Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)

          • Changes:
            • New user interface unified in EM Navigator, Yorodumi & Omokage search, supporting mobile devices as well as PCs.
            • New Yorodumi replace the individual data page ("Detail page" of EM Navigator in the legacy system). It is unified browser for EMDB, PDB, and SASBDB entries integrated with EM Navigator and Omokage search.
            • The viewers (structure/movie viewers) appear in pop-up windows. On a PC, multiple viewer windows can be opened. On mobile devices, the viewers support touch operation.
          • New features:
            • Molmil, molecular structure viewer, and SurfView, surface model viewer for EMDB map data, are available to view the 3D structures. Both viewers support mobile device use.
            • Yorodumi support SASBDB entries.
            • Some new pages such as Yorodumi Papers, citation database of structure data entries and Yorodumi Search, cross search by keywords

          Related info.: EM Navigator (legacy version) / EM Navigator / Yorodumi (legacy version) / Yorodumi / SurfView / Molmil / Movie viewer / EMN Papers / Yorodumi Papers / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi

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          Information from PDBMLplus

          PDBMLplus is the XML format file including additional information relating to individual proteins. Currently, PDB files are lacking a detailed description of function, experimental conditions, and the like. And then such information was included to extended XML database, named PDBMLplus.

          Related info.: PDBj

          External links: PDBMLplus - PDBj helip / About Functional Details page

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          Yorodumi annotation

          Annotation by Yorodumi/EM Navigator manager

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

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          About Yorodumi Docs

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          Yorodumi Docs

          Documentation for Yorodumi, EM Navigator, Omokage, etc.

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