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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

Major update of PDB

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Jun 16, 2017. Omokage search with filter

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Sep 15, 2016. EM Navigator & Yorodumi renewed

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

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Apr 13, 2016. Omokage search got faster

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Mar 3, 2016. Presentation PDF file for IPR seminar on Feb 19.

Presentation PDF file for IPR seminar on Feb 19.

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Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.?

A: in semi-automatic process with UCSF Chimera

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A: We are making them by full-automatic process using Jmol. Their styles are depend on the data type

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Yorodumi

Thousand views of thousand structures

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Covid-19 info

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F&H Search

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Jmol/JSmol

An open-source viewer for chemical structures in 3D

  • Mouse/touch operation
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External links:Jmol: an open-source Java viewer for chemical structures in 3D

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Molmil

WebGL based molecular viewer

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

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

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Carbohydrate representation

Polysaccaride/carbohydrate data representation in PDB

  • In July 2020, representation for polysaccaride/carbohydrate information in PDB is improved.
  • The polysaccaride figures are generated by GlycanBuilder2.
  • See following external links for details.

External links:Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans - ScienceDirect / GlycanBuilder2 - RINGS (Resource For INformatics Of Glycomes at Soka) / Carbohydrate Remediation - wwPDB documentation / Coming July 29: Improved Carbohydrate Data at the PDB - wwPDB news

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Experimental methods, equipments, and software data

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Changes in new EM Navigator and Yorodumi

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

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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.

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