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New PDB archive reference paper now in NAR 2019 Database issue (wwPDB news)
Created: 2018-12-05
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Co-Creation Bureau, Osaka University "Enjoy with Osaka Univ."

In this event, we exhibit booths and experience corners to introduce various study, result, and resources of Osaka University in the event site. From children to adults, various people can learn science and study with enjoying. No registration is necessary. Please feel free to come!

Date and Time:
  • 17th Nov 2018 (Sat): 11:00 - 17:00 (JST)
Venue:
Lalaport EXPOCITY (Suita, Osaka, Japan) about two minutes from Banpaku Kinen Koen Osaka Monorail Station by walk
2nd Floor, near by Hikari plaza

"Shape" of proteins, which supporting the life

We provide various menus that help to realize the diversity and importance of the shape of protein via many types of experience such as watching, touching and making. We hope they promote to understand to biomolecules. In detail, we exhibit the following menus:
  1. Watching: View various protein molecules sterically via computer graphic (CG) by accessing the PDBj web site.
  2. Touching: Touch the molecule models made from the 3D printer.
  3. Making: Make molecule models from paper.
We also introduce the technologies to solve the shape, such as synchrotron and cryo-electron microscopy.
Co-Creation Bureau, Osaka University "Enjoy with Osaka Univ." leaflet
Created: 2018-11-02 (last edited: 3 months ago)2018-11-02
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Science Agora 2018 - in Tokyo -

Science Agorais an event to find something fun or curious about science, enjoy and discuss together, and share the experience. In this year, it is held from 9th Nov 2018 (Fri) to 11th Nov 2018 (Sun) (JST). The venue is around Odaiba, Tokyo, Japan. We exhibit a booth in this event.
Exhibition date and time:
  • 10th Nov 2018 (Sat) and 11th (Sun) 10:00 - 16:00 (JST)
Venue:
4th Floor, No. 35

"Shape" of proteins, which supporting the life

We provide various menus that help to realize the diversity and importance of the shape of protein via many types of experience such as watching, touching and making. We hope they promote to understand to biomolecules. In detail, we exhibit the following menus:
  1. Watching: View various protein molecules sterically via computer graphic (CG) by accessing the PDBj web site.
  2. Touching: Touch the molecule models made from the 3D printer.
  3. Making: Make molecule models from paper.
We also introduce the technologies to solve the shape, such as synchrotron and cryo-electron microscopy.
"Science Agora 2018" leaflet
Created: 2018-11-02
This page is also available in: 日本語
The PDBj web interface uses the beta version of Molmil 2, an enhanced version of the current Molmil, from November 1st 2018 by default. To keep using the old Molmil 1 interface, please select "Molmil 1" under the default selected viewer on the customizations page.

Molmil 2 is also available as a standalone viewer at https://pdbj.org/molmil2/. After development of Molmil 2 has been finished, the URL of the stable standalone version of Molmil, i.e. https://pdbj.org/molmil/ will also refer to Molmil 2. Molmil 2 is expected to enter a stable status around April or May 2019.
The current standalone version of Molmil, i.e. Molmil 1, will remain accessible from https://pdbj.org/molmil1/.

Please inform us if you experience any problems with Molmil 2.
Created: 2018-11-01
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OneDep Improves Support for Deposition of XFEL/SFX Structures (wwPDB news)
Created: 2018-10-03
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The mmJSON files previously accessible via our REST interface are now also accessible from our ftp site.

For more information, please refer to our mmJSON help page.
Created: 2018-09-28
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PDB Certified as a Trustworthy Data Repository (wwPDB news)
Created: 2018-09-12 (last edited: 5 months ago)2018-09-12
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Depositing a Structure? Include Your ORCiD (wwPDB news)
Created: 2018-07-23
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ORCIDs to become mandatory for OneDep contact authors (wwPDB news)
Created: 2018-06-27 (last edited: 7 months ago)2018-06-27
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Improvements to Data Replacement Prior to Release; Privacy Policy Update (wwPDB news)
Created: 2018-05-25
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Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures (wwPDB news)
Created: 2018-05-10 (last edited: 9 months ago)2018-05-10
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Protein Structures Sought for CASP13 (wwPDB news)
Created: 2018-04-12 (last edited: 10 months ago)2018-04-12
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Access Updated Validation Reports for PDB Structures (wwPDB news)
Created: 2018-03-29
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wwPDB Biocuration Highlighted in New Publication (wwPDB news)
Created: 2018-02-22 (last edited: 11 months ago)2018-02-22
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We announce the new version of jV, Java based molecular viewer, was released. The latest version is 4.5.4.

There is no functional change compared to the previous version. Only the certification for signing was updated.

In some cases update procedure is required in the web site embedded Java applets. See below for details.

Type of use Update Comments
Binary (jar) version Not necessary This type runs the jar file that downloaded in the local system beforehand. It is not necessary to update because there is no change in functional specification and no confirmation is required on running in local system. However it is no harmful when updated.
Java Web Start (jnlp) version Not necessary This type runs the latest version of software downloaded from Internet each the execution time. Any procedures are not necessary at the user side because the server always provides the latest version.
Java applet in the web site (*1) Updating is necessary when it refers the jV software placed by oneself.

When the Java applet embedded in the web site refers the jV software placed by oneself, it is necessary to update the placed jV. Otherwise launching the jV will fail because the certificate expired.

*1: Currently, some latest web browsers such as Firefox and Google Chrome are no longer support Java applets.

Created: 2018-02-08
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Time-stamped Copies of the PDB Archive Available (wwPDB news)
Created: 2018-01-11 (last edited: more than 1 year ago)2018-01-11
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