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Integrate Molmil

... integrate molmil on your own website. The following example is a simple webpage including the required JavaScript to load and initialize ... Alternatively, it is also possible to integrate molmil using a simple iframe and using molmil commands to load and ...

News on 2014-12-24

Beginning at 9:00 a.m. on January 27, 2015 (JST) crystal structures should be submitted using ... . Improvements to this system are regularly incorporated based on user feedback. As a result of this successful release, RCSB PDB and PDBj will only accept ...

Chemical shift

... ://bmrb.pdbj.org/validate/ Chemical shift files are stored in a new directory path, grouped by the middle two characters of the ... _shifts/. All of these data files are symbolically linked to a single directory: ftp://ftp.wwpdb.org/pub/pdb/data/structures/ ...

sequence-representative

... scores for all pairs of structures. The pairs which score above a certain threshold (Sequence identity30% and E-value0.1) arelinked. ... structure with the greatest number of links is chosen, and a new cluster defined with it as the representative and all of ...

RMSD

RMSD stands for root mean square deviation. It is a commonly used measure of dissimilarity or error in protein structure. For ... two sets of points and a mapping between those points the RMSD is defined to be the square ...

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

... microscopy. He has joined PDB in 2010 and has established himself as a highly qualified professional with deep understanding of scientific data and various experimental ...

News on 2010-07-13

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[wwPDB] Updated Validation Reports for Released PDB Structures

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[wwPDB] Extension to EMDB Accession Codes

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[wwPDB] PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

... and processed by the PDB-Dev system. Each IHM structure is issued a PDB ID, reported in the PDBx/mmCIF file in the _database_2 ...

News on 2004-09-01

We start a new service, Sequence Navigator, to allow searching for homologous proteins using the amino acid sequence.

News on 2004-11-12

PDBj starts a new service in xPSSS to display the Electron Density Map of each biological macromolecule, whose structure factor file has been deposited, through the Summary page or the Experimental Details page of xPSSS.

[wwPDB] PDB50: Registration Open for Virtual Event

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News on 2009-01-23

... / We will keep ftp://pdb.protein.osaka-u.ac.jp/v3/ as a symbolic link to (updated) ftp://pdb.protein.osaka-u.ac.jp/ in ...

[wwPDB] Distribution of Electron Microscopy metadata in PDBx/mmCIF file format

... entries released before October 2023 will have PDBx/mmCIF files added at a later date. The description of PDBx/mmCIF categories and items featured in ...

[wwPDB] wwPDB EM Validation Reports Now Publicly Available

... include images for deposited masks, improved map-model overlay images, visualization of a (approximate) raw map from two half-maps, and rotationally averaged power spectrum ...

Notice of Service Suspension (ASH, DASH, SeSAW, MAFFTash, Spanner, SFAS)

Due to a lack of IT personnel, the following services are now suspended. - ASH - DASH - SeSAW - MAFFTash - Spanner - SFAS

[wwPDB] Tribute to Dr. Olga Kennard

... Kennard at the PDB-SwissProt Symposium in Jerusalem in 1996. Olga was a person of great integrity and drive and, in an age before computers ...

[wwPDB] PDB-Dev now PDB-IHM

... to compute their three-dimensional structures. PDB-IHM (formerly PDB-Dev) is a system for archiving and disseminating structures determined using integrative or hybrid methods ...

[wwPDB] Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

... /mmCIF and PDBML formats (see previous announcement). In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never ...

Spanner

... of the Spanner web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

[wwPDB] Future Planning: Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only

... characters prefixed by ‘PDB’, e.g., pdb_00001abc. Each PDB ID has a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals ...

EMDB header format to be updated to v.1.9.0

... .pdbj.org/pub/emdb/doc/XML-schemas/Header-schema/candidate/emdb.xsd . A complete list of changes can be found at the beginning of the ...

SFAS

... of the SFAS web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

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PDB entries from 2025-07-09

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