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News (10)

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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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    Yorodumi Docs

    Documentation for Yorodumi, EM Navigator, Omokage, etc.

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