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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

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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

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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 (12)

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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.
    • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

    Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / 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 / Experimental methods, equipments, and software data / Function and homology information / 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

        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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        Experimental methods, equipments, and software data

        Database of experimental methods of EMDB, PDB and SABDB.

        Related info.: Comparison of 3 databanks / Yorodumi Search

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        Function and homology information

        Molecular function, domain, and homology information from related databases.

      • To help to understand the molecular function and to find the related structure data, Yorodumi and Yorodumi Search display and utilize the related database information about function and homology. In addition to the information of EC, EMBL, GeneBank, GO, InterPro, UniProt, etc. stored in the EMDB header XML, PDBx/mmCIF and sasCIF original data, information of Pfam, PROSITE, Reactome, UniProkKB, etc. are collected via PDBMLplus, EMDB-PDB fitting data, and/or UniProt.
      • Related info.: Information from PDBMLplus / Yorodumi Search / Yorodumi

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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 / 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 / Function and homology information

        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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