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News (13)

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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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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Dec 4, 2015. The article about Omokage search is published online

The article about Omokage search is published online

Related info.: Omokage search / gmfit

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Nov 28, 2015. Omokage search starts to support SASBDB models

Omokage search starts to support SASBDB models

  • Models data in SASBDB are added to the Omokage search database.
  • SASBDB is a databank for small angle scattering data
  • A SASBDB model can be used as a search query.
  • The search result may include SASBDB models.

Related info.: Omokage search / SASBDB / Comparison of 3 databanks

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Dec 10, 2014. PDB "SPLIT" entries are replaced with "LARGE" entries

PDB "SPLIT" entries are replaced with "LARGE" entries

  • Structure data deposited as multiple PDB entries are replace with single combined entries, which were previously stored as "large structure". See here for details.
  • In EM Navigator, many ribosome and several virus entries are replaced.

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Sep 22, 2014. New service: Omokage search

New service: Omokage search

  • Shape similarity search service, Omokage search has started.
  • Related info.: Omokage search

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    Mar 30, 2013. New page of in EM Navigator, statistics

    New page of in EM Navigator, statistics

    Related info.: EMN Statistics

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    Jan 16, 2013. New EMDB header format

    New EMDB header format

    • Format of the EMDB header file (XML based meta data file, not the map data themselves) are updated to version 1.9 (see here for details)
    • Now, the contents of EM Navigator are based on the new data. Colors of some parts (e.g. bars in top area of the Detail pages) indicate 3D-reconstruction method, instead of 'aggregation states'.

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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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    Information (30)

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    EM Navigator

    3D electron microscopy data browser

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

    • Browser for 3D electron microscopy (3D-EM) data of biological molecules and assemblies.

    Related info.: EMDB / PDB / PDBj / Q: What is the data source of EM Navigator? / EMN Search / EMN Papers / EMN Gallery / EMN Statistics / Changes in new EM Navigator and Yorodumi

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    EM Navigator (legacy version)

    Legacy version of EM Navigator

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

    • EM Navigator is the web site to browse 3D electron microscopy (3D-EM) data of biological molecules and assemblies.
    • The data are based on EMDB and PDB data.(statistics)
    • This is for non-specialists, beginners, and experts in 3D-EM or structural/molecular biology.
    • run by PDBj

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

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    EMN Search

    3DEM data search

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

    • Advanced data search for EMDB and EM data in PDB widh various search and display options

    Related info.: EMDB / PDB / EM Navigator / Q: What is the data source of EM Navigator? / Yorodumi Search

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    EMN Papers

    Database of articles cited by 3DEM data entries

    URL: https://pdbj.org/emnavi/pap.php?em=1

    • Database of articles cited by 3DEM data entries in EMDB and PDB
    • Using PubMed data

    Related info.: EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

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    EMN Gallery

    Image gallery of 3DEM data

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

    • Categorization is done by EM Navigator manager manually. It is not strict.

    Related info.: EMDB / PDB / EM Navigator

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    EMN Statistics

    Statistics of 3DEM data in table and graph styles

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

    • The table can be sorted. Click the column header to be sorted. (second click to reverse, [Shift]+click for multi-column sort)
    • To show the bar graph in table mode, point the column/row header by mouse courser.
    • To search the correspoinding data, click the cell of value.
    • Examples:

    Related info.: EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Mar 30, 2013. New page of in EM Navigator, statistics

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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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        Omokage search

        Search structure by SHAPE

        URL: https://pdbj.org/omokage/

        • "Omokage search" is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.
        • The search is performed ageinst >200,000 structure data, which consists of EMDB map data, PDB coordinates (deposited units (asymmetric units, usually), PDB biological units, and SASBDB mdoels).
        • For the search query, you can use either a data in the PDB/EMDB/SASBDB or your original model.
        • Supported formats are PDB (atomic model, SAXS bead model, etc.) and CCP4/MRC map (3D density map).
        • Shape comparison is performed by iDR profile method, which uses 1D-distance profiles of super-simplified models generated by vector quantizaion in Situs package.

        Related info.: Comparison of 3 databanks / Sep 22, 2014. New service: Omokage search / gmfit / Re-ranking by gmfit

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        Yorodumi Docs

        Documentation for Yorodumi, EM Navigator, Omokage, etc.

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

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          Movie viewer

          Visualization of 3DEM structure data by movies.

          • Horizontal- and vertical- rotation motions and "slicing" motion are recorded in the movies.
          • As the movie frame can be controlled by mouse/touch position, it can be operated interactively as a molecular viewer. According to the mouse/finger position and orientation of the motion on the movie panel, the model rotates on horizontal or vertical direction. By horizontal mouse/finger movement on the top part of the movie, the slicing motion is shown.

          Related info.: Q: How do you make the movies in EM Navigator? / Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations? / SurfView / Changes in new EM Navigator and Yorodumi

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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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          SurfView

          EMDB map surface models viewer on Web browsers

          • SurfView run on Web browser on a smartphone or tablet device as well as PC. (SurfView is based on a WebGL and three.js, Javascript 3D library)
          • The surface models shwon in this viewer are modified for simplification and data size reduction. To get views of full-resolution data, see movies instead.
          • Mouse/touch operation
            X-Y rotationX-Y moveZoom in/out
            Mouseleft dragright dragcenter drag / wheel
            Touchsingle fingerdouble fingerpinch

          Related info.: Movie viewer / Molmil / Changes in new EM Navigator and Yorodumi

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          Comparison of 3 databanks

        • Yorodumi and Omokage can cross-search these DBs.
          PDBEMDBSASBDB
          methodvarious3DEMSAS (Small Angle Scattering)
          main dataatomic model3D mapSAS profile (+/- 3D models)
          str. data formatPDBx/mmCIF, etc.CCP4 mapPDB + sasCIF
          meta data formatPDBx/mmCIF, etc.EMDB XMLASCII + sasCIF
        • Related info.: EMDB / PDB / SASBDB / Omokage search

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          EMDB

          Electron Microscopy Data Bank, Databank for 3DEM

          URL: http://emdatabank.org/

          Related info.: 3D electron microscopy (3DEM) / Comparison of 3 databanks

          External links: EMDataBank.org / The Electron Microscopy Data Bank (PDBe site) / EM Data Bank - Wikipedia

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          PDB

          Protein Data Bank - The single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

          URL: http://wwPDB.org/

          Related info.: PDBj / Comparison of 3 databanks

          External links: World Wide PDB

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          PDBj

          Protein Data Bank Japan.

          URL: http://pdbj.org/

        • A member of wwPDB.
        • Related info.: PDB / Information from PDBMLplus

          External links: PDBj@Facebook / PDBj@Twitter / Haruki Nakamura Lab., Institute of Protein Research,Osaka University

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          SASBDB

          Small Angle Scattering Biological Data Bank - Curated repository for small angle scattering data and models

          URL: http://www.sasbdb.org/

          • Develop & manage: BioSAXS group in EMBL
          • Since 2014

          Related info.: Comparison of 3 databanks

          External links: Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI. SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res. 2015 Jan 28;43:D357-63.

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          gmfit

          a program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)

          URL: http://strcomp.protein.osaka-u.ac.jp/gmfit/

          • Developed by Takeshi Kawabata in IPR, Osaka-univ.
          • Used from Omokage search.

          Related info.: Omokage search / Dec 4, 2015. The article about Omokage search is published online / Re-ranking by gmfit

          External links: Pairwise gmfit

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          3D electron microscopy (3DEM)

          A generic term of electron microscopic analyses to obtain 3D structures

          • Analyses such as electron tomography, single particle analysis, and electron diffraction are included.
            Aggregation statesMethods generally used
            "individual structure"electron tomography
            "single particle"single particle analysis
            "icosahedral"single particle analysis
            "helical"helical reconstruction / single particle analysis
            "2D-crystal"electron diffraction / Fourier filtering
          • Characteristics compared to X-ray crystallography and NMR:
            • Advantage: Wider applicability of sample (not require high-purity or high-concentration smaple, and useful for more huge, complex, flexible, and less uniform sample)
            • Disadvantage: Lower resolution (hard to get atomic-level resolution data)

          Related info.: EMDB / electron cryo microscopy (cryoEM)

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          electron cryo microscopy (cryoEM)

          Electron microscopy where the sample is studied at cryogenic temperatures

        • The specimen is cooled at 4~100K (-269~-170℃) to keep it in hydrated state in the highly vaqumed environment, and to reduce radiation dammage by electron beam.
        • Related info.: 3D electron microscopy (3DEM) / Q: Is 3DEM same as electron cryo microscopy (cryoEM)?

          External links: Cryo-electron microscopy - Wikipedia

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          "Movies out of date"

          Movies with this annotation may not be up-to-date.

        • EMDB map data are sometimes remediated. Unfortunately, the process of making movies in the EM Navigaotr are not fully automated, and it is very hard to remake the all to catch up. So, some movies and movie parameters are based on the older data, and may be improper for new map data.
        • Related info.: Q: How do you make the movies in EM Navigator?

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          Re-ranking by gmfit

          The similarity ranking by Omokage search can be re-ordered according to correlation coefficient by gmfit, expecting incorporation of the (potential) benefits of two methods with following properties.

          • MethodSpeedPotential accuracy
            Omokage search
            (iDR profile comparison)
            ++
            (sub-msec / 1 comparison)
            -
            (1D profile comparison)
            gmfit
            (Gaussian mixture model fitting)
            +
            (sub-sec / 1 comparison)
            +
            (comparison in 3D space)

          Related info.: gmfit / Omokage search

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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.

            Read more