-Search & filter documents
+Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
+Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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.
+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
+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
+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
+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
+Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.
+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.
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.?
+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
- 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.
- 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.
- 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?
Thousand views of thousand structures
- 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
Cross-search of EMDB, PDB, SASBDB, etc.
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
Database of articles cited by EMDB/PDB/SASBDB data
- 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
Taxonomy data in EMDB/PDB/SASBDB
- Taxonomy database of sample sources of data in EMDB/PDB/SASBDB
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Mar 5, 2020. Novel coronavirus structure data
Documentation for Yorodumi, EM Navigator, Omokage, etc.
Page for Covid-19 featured contents.
Related info.:Comparison of 3 databanks / Aug 12, 2020. New: Covid-19 info
An open-source viewer for chemical structures in 3D
|X-Y rotation||X-Y move||Zoom in/out|
|Mouse||left drag||[Ctrl] + right drag||center drag (vertical) / wheel|
|Touch||single finger||double finger||pinch|
Related info.:Molmil / Yorodumi
WebGL based molecular viewer
- Mouse/touch operation
X-Y rotation X-Y move Zoom in/out Mouse left drag center drag / shift + left drag right drag / wheel Function menu: top left buttons on viewer screen Touch single finger pinch
Related info.:Jmol/JSmol / SurfView / Changes in new EM Navigator and Yorodumi
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. (Article)
- See following external links for other details.
+Experimental methods, equipments, and software data
Database of experimental methods of EMDB, PDB and SABDB.
Related info.:Comparison of 3 databanks / Yorodumi Search
+Function and homology information
Molecular function, domain, and homology information from related databases.
Related info.:Information from PDBMLplus / Yorodumi Search / Yorodumi
+Changes in new EM Navigator and Yorodumi
Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)
- 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
+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
Annotation by Yorodumi/EM Navigator manager
Related info.:Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?
-About Yorodumi Docs
Documentation for Yorodumi, EM Navigator, Omokage, etc.