Register for the Oct 22 Virtual Office Hour:
Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Learn how to prepare for the July 21, 2027 transition, including using shortlinks in your code
www.rcsb.org/news/fe...
Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Learn how to prepare for the July 21, 2027 transition, including using shortlinks in your code
www.rcsb.org/news/fe...
September 24, 2026 at 4:55 PM
Register for the Oct 22 Virtual Office Hour:
Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Learn how to prepare for the July 21, 2027 transition, including using shortlinks in your code
www.rcsb.org/news/fe...
Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Learn how to prepare for the July 21, 2027 transition, including using shortlinks in your code
www.rcsb.org/news/fe...
This is absolutely beautiful! 😍
🧬 ProteinView — explore proteins, DNA and small molecules in the terminal!
💯 Explore PDB/mmCIF structures, multiple visualization modes & interface analysis
🦀 Written in Rust & built w/ @ratatui.rs
⭐ GitHub: github.com/001TMF/Prote...
#rustlang #ratatui #tui
🧬 ProteinView — explore proteins, DNA and small molecules in the terminal!
💯 Explore PDB/mmCIF structures, multiple visualization modes & interface analysis
🦀 Written in Rust & built w/ @ratatui.rs
⭐ GitHub: github.com/001TMF/Prote...
#rustlang #ratatui #tui
September 12, 2026 at 9:24 AM
This is absolutely beautiful! 😍
🧬 ProteinView — explore proteins, DNA and small molecules in the terminal!
💯 Explore PDB/mmCIF structures, multiple visualization modes & interface analysis
🦀 Written in Rust & built w/ @ratatui.rs
⭐ GitHub: github.com/001TMF/Prote...
#rustlang #ratatui #tui
🧬 ProteinView — explore proteins, DNA and small molecules in the terminal!
💯 Explore PDB/mmCIF structures, multiple visualization modes & interface analysis
🦀 Written in Rust & built w/ @ratatui.rs
⭐ GitHub: github.com/001TMF/Prote...
#rustlang #ratatui #tui
Guide to Understanding PDB Data: Beginner’s Guide to PDBx/mmCIF
PDB101: Learn: Guide to Understanding PDB Data: Beginner’s Guide to PDBx/mmCIF
PDBx/mmCIF forms the basis of wwPDB data deposition, annotation, and archiving of PDB structure data. This PDB-101 resource is an introductory guide.
pdb101.rcsb.org
September 9, 2026 at 4:44 PM
Guide to Understanding PDB Data: Beginner’s Guide to PDBx/mmCIF
Paper Published about the PDB Beta Archive
Read about changes that will become the default on July 21, 2027. Transition to this new architecture today.
Read about changes that will become the default on July 21, 2027. Transition to this new architecture today.
Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution
wwPDB has extended PDB IDs to 12 characters with a prefix `pdb_' followed by eight alphanumeric characters in lower case (for example pdb_1000axyz). A beta version of the PDB Archive (https://files-beta.wwpdb.org), with extended PDB IDs and an improved directory structure, is now available to help communities adopt extended PDB IDs and the PDBx/mmCIF format.
journals.iucr.org
August 24, 2026 at 6:33 PM
Paper Published about the PDB Beta Archive
Read about changes that will become the default on July 21, 2027. Transition to this new architecture today.
Read about changes that will become the default on July 21, 2027. Transition to this new architecture today.
🚨Get ready for the future of the PDB Archive!
A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition.
📄Read here: journals.iucr.org/d/issues/202...
#PDB
A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition.
📄Read here: journals.iucr.org/d/issues/202...
#PDB
Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution
wwPDB has extended PDB IDs to 12 characters with a prefix `pdb_' followed by eight alphanumeric characters in lower case (for example pdb_1000axyz). A beta version of the PDB Archive (https://files-be...
journals.iucr.org
August 18, 2026 at 8:12 AM
🚨Get ready for the future of the PDB Archive!
A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition.
📄Read here: journals.iucr.org/d/issues/202...
#PDB
A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition.
📄Read here: journals.iucr.org/d/issues/202...
#PDB
Watch the Virtual Office Hour on Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Learn how to prepare for the July 21, 2027 transition, including using shortlinks to in your code.
Learn how to prepare for the July 21, 2027 transition, including using shortlinks to in your code.
Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Starting July 21, 2027,
– New PDB depositions will only be assigned extended PDB IDs, e.g., pdb_1000abc
– These new entries will only be available in PDBx/mmCIF format and will have a new DOI syntax
– The PDB archive will be re-organized based on extended PDB IDs (including file names and directorie
www.youtube.com
August 7, 2026 at 4:55 PM
Watch the Virtual Office Hour on Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
Learn how to prepare for the July 21, 2027 transition, including using shortlinks to in your code.
Learn how to prepare for the July 21, 2027 transition, including using shortlinks to in your code.
Out now in Journal of Applied Crystallography: mmCIF Validator, automated validation of mmCIF files against the PDBx/mmCIF dictionary
Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI)
Paper: doi.org/10.1107/S160...
Code: github.com/PDBeurope/mm...
Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI)
Paper: doi.org/10.1107/S160...
Code: github.com/PDBeurope/mm...
mmCIF Validator: a comprehensive validation tool for structural biology data files
The mmCIF Validator provides real-time automated validation of mmCIFs against a valid PDBx/mmCIF dictionary. The validator is available as both a Visual Studio Code extension and a standalone Python s...
doi.org
August 6, 2026 at 7:41 AM
Out now in Journal of Applied Crystallography: mmCIF Validator, automated validation of mmCIF files against the PDBx/mmCIF dictionary
Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI)
Paper: doi.org/10.1107/S160...
Code: github.com/PDBeurope/mm...
Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI)
Paper: doi.org/10.1107/S160...
Code: github.com/PDBeurope/mm...
I honestly wish the folks developing AI protein design and structure prediction tools would learn how to FORMAT A FRICKING MMCIF FILE correctly.
August 1, 2026 at 3:10 AM
I honestly wish the folks developing AI protein design and structure prediction tools would learn how to FORMAT A FRICKING MMCIF FILE correctly.
wwPDB News: The refactored “Based on previous” workflow allows depositors to selectively import and reuse mmCIF metadata from a previously deposited PDB entry with method-aware safeguards, macromolecule checks, ORCID search, and transparent import logging.
Reuse Metadata from Previous PDB Depositions
The refactored “Based on previous” workflow allows depositors to selectively import and reuse mmCIF metadata from a previously deposited PDB entry with method-aware safeguards, macromolecule checks, ORCID search, and transparent import logging.
www.rcsb.org
July 29, 2026 at 4:43 PM
wwPDB News: The refactored “Based on previous” workflow allows depositors to selectively import and reuse mmCIF metadata from a previously deposited PDB entry with method-aware safeguards, macromolecule checks, ORCID search, and transparent import logging.
An mmCIF file can say a residue has two alternate conformations and how often each appears. It cannot say which alternates occur together in the same copy. A draft proposal for recording that correlation, plus a tool to inspect it: diffuse.science/posts/mmcif-...
mmCIF Explorer and the Heterogeneity Proposal
A playground for the PDBx/mmCIF file exploration, a look at the current proposal for encoding correlated heterogeneity
diffuse.science
July 29, 2026 at 3:24 AM
An mmCIF file can say a residue has two alternate conformations and how often each appears. It cannot say which alternates occur together in the same copy. A draft proposal for recording that correlation, plus a tool to inspect it: diffuse.science/posts/mmcif-...
💎 We hear the wwPDB exhibit at #IUCr2026 may have something that would make friendship bracelet fans proud... and yes, it's PDBx/mmCIF compliant. 😉
You'll have to see it for yourself.
👉 Register: event.fourwaves.com/...
#Crystallography #wwPDB #Calgary2026
You'll have to see it for yourself.
👉 Register: event.fourwaves.com/...
#Crystallography #wwPDB #Calgary2026
July 23, 2026 at 1:55 PM
💎 We hear the wwPDB exhibit at #IUCr2026 may have something that would make friendship bracelet fans proud... and yes, it's PDBx/mmCIF compliant. 😉
You'll have to see it for yourself.
👉 Register: event.fourwaves.com/...
#Crystallography #wwPDB #Calgary2026
You'll have to see it for yourself.
👉 Register: event.fourwaves.com/...
#Crystallography #wwPDB #Calgary2026
Big PDB Changes Are One Year Away!
On July 21, 2027, wwPDB will fully transition to extended PDB IDs for new depositions and the
PDB archive will use a new directory structure based on 12-character extended PDB IDs. Visit wwpdb.org for details.
On July 21, 2027, wwPDB will fully transition to extended PDB IDs for new depositions and the
PDB archive will use a new directory structure based on 12-character extended PDB IDs. Visit wwpdb.org for details.
July 21, 2026 at 4:44 PM
Big PDB Changes Are One Year Away!
On July 21, 2027, wwPDB will fully transition to extended PDB IDs for new depositions and the
PDB archive will use a new directory structure based on 12-character extended PDB IDs. Visit wwpdb.org for details.
On July 21, 2027, wwPDB will fully transition to extended PDB IDs for new depositions and the
PDB archive will use a new directory structure based on 12-character extended PDB IDs. Visit wwpdb.org for details.
🚨 Big PDB changes are one year away
Starting July 21, 2027:
▪ PDB Beta Archive becomes the main archive.
▪ Extended PDB IDs and PDBx/mmCIF will be the standard.
Start using extended IDs and PDBx/mmCIF today!
🔗 www.wwpdb.org/news/news?ye...
#PDB #StructuralBiology
Starting July 21, 2027:
▪ PDB Beta Archive becomes the main archive.
▪ Extended PDB IDs and PDBx/mmCIF will be the standard.
Start using extended IDs and PDBx/mmCIF today!
🔗 www.wwpdb.org/news/news?ye...
#PDB #StructuralBiology
Big PDB Changes Are One Year Away: Extended PDB IDs, the PDB Beta Archive, and PDBx/mmCIF
wwPDB: Worldwide Protein Data Bank
www.wwpdb.org
July 21, 2026 at 8:38 AM
🚨 Big PDB changes are one year away
Starting July 21, 2027:
▪ PDB Beta Archive becomes the main archive.
▪ Extended PDB IDs and PDBx/mmCIF will be the standard.
Start using extended IDs and PDBx/mmCIF today!
🔗 www.wwpdb.org/news/news?ye...
#PDB #StructuralBiology
Starting July 21, 2027:
▪ PDB Beta Archive becomes the main archive.
▪ Extended PDB IDs and PDBx/mmCIF will be the standard.
Start using extended IDs and PDBx/mmCIF today!
🔗 www.wwpdb.org/news/news?ye...
#PDB #StructuralBiology
The DiffUSE Project wants examples where structural heterogeneity matters but cannot be encoded in PDBx/mmCIF. X-ray, cryo-EM, time-resolved, multi-map, or fragment screening data welcome. Submit yours: diffuse.science/submit/
Submit Examples of Heterogeneous Structural Data
The DiffUSE Project
diffuse.science
May 28, 2026 at 2:12 AM
The DiffUSE Project wants examples where structural heterogeneity matters but cannot be encoded in PDBx/mmCIF. X-ray, cryo-EM, time-resolved, multi-map, or fragment screening data welcome. Submit yours: diffuse.science/submit/
May is National Pet Month.
Cats Iris (tortoise) and Ares (grey) help RCSB PDB's Ezra Peisach manage the PDBx/mmCIF Dictionary and preparations for the upcoming transition to extended PDB IDs and the new Beta Archive www.rcsb.org/news/fe...
Cats Iris (tortoise) and Ares (grey) help RCSB PDB's Ezra Peisach manage the PDBx/mmCIF Dictionary and preparations for the upcoming transition to extended PDB IDs and the new Beta Archive www.rcsb.org/news/fe...
May 21, 2026 at 4:34 PM
May is National Pet Month.
Cats Iris (tortoise) and Ares (grey) help RCSB PDB's Ezra Peisach manage the PDBx/mmCIF Dictionary and preparations for the upcoming transition to extended PDB IDs and the new Beta Archive www.rcsb.org/news/fe...
Cats Iris (tortoise) and Ares (grey) help RCSB PDB's Ezra Peisach manage the PDBx/mmCIF Dictionary and preparations for the upcoming transition to extended PDB IDs and the new Beta Archive www.rcsb.org/news/fe...
Register for the June 1 Office Hour on Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
This Office Hour is for all users, but particularly for software developers and journal editors.
Details: pdb101.rcsb.org/news...
This Office Hour is for all users, but particularly for software developers and journal editors.
Details: pdb101.rcsb.org/news...
May 4, 2026 at 4:44 PM
Register for the June 1 Office Hour on Transitioning to the New PDB Beta Archive, Extended PDB IDs, and PDBx/mmCIF
This Office Hour is for all users, but particularly for software developers and journal editors.
Details: pdb101.rcsb.org/news...
This Office Hour is for all users, but particularly for software developers and journal editors.
Details: pdb101.rcsb.org/news...
🚨July 21, 2027: PDB Beta Archive replaces current PDB archive.
Key updates:
• Extended IDs (1ABC → pdb_00001abc).
• Only 12-char IDs issued.
• Data in PDBx/mmCIF & PDBML only.
All PDB users must transition to extended IDs and PDBx/mmCIF.
www.wwpdb.org/news/news?ye...
#PDB
Key updates:
• Extended IDs (1ABC → pdb_00001abc).
• Only 12-char IDs issued.
• Data in PDBx/mmCIF & PDBML only.
All PDB users must transition to extended IDs and PDBx/mmCIF.
www.wwpdb.org/news/news?ye...
#PDB
April 27, 2026 at 12:36 PM
🚨July 21, 2027: PDB Beta Archive replaces current PDB archive.
Key updates:
• Extended IDs (1ABC → pdb_00001abc).
• Only 12-char IDs issued.
• Data in PDBx/mmCIF & PDBML only.
All PDB users must transition to extended IDs and PDBx/mmCIF.
www.wwpdb.org/news/news?ye...
#PDB
Key updates:
• Extended IDs (1ABC → pdb_00001abc).
• Only 12-char IDs issued.
• Data in PDBx/mmCIF & PDBML only.
All PDB users must transition to extended IDs and PDBx/mmCIF.
www.wwpdb.org/news/news?ye...
#PDB
We just tried to submit mmCIF coordinates of some predicted protein structures to a journal as supplemental data, & they said they could not handle the files unless we turned them into Word or pdf files. Why do we pay for journals to publish our papers when such incompetence and ignorance prevails?
April 21, 2026 at 10:18 PM
We just tried to submit mmCIF coordinates of some predicted protein structures to a journal as supplemental data, & they said they could not handle the files unless we turned them into Word or pdf files. Why do we pay for journals to publish our papers when such incompetence and ignorance prevails?
Added a residue annotation tool to coot1-trimmings. Allows you to save notes associated with the active residue. These can then be written to (and reloaded from) the mmcif:
March 30, 2026 at 6:19 PM
Added a residue annotation tool to coot1-trimmings. Allows you to save notes associated with the active residue. These can then be written to (and reloaded from) the mmcif:
Custom dictionary support is available in the PDBe mmCIF validator:
VS Code: set dictionary path in settings
Python script: pass dictionary path via CLI
#mmCIF #PDB #Bioinformatics #StructuralBiology
VS Code: set dictionary path in settings
Python script: pass dictionary path via CLI
#mmCIF #PDB #Bioinformatics #StructuralBiology
March 27, 2026 at 11:04 AM
Custom dictionary support is available in the PDBe mmCIF validator:
VS Code: set dictionary path in settings
Python script: pass dictionary path via CLI
#mmCIF #PDB #Bioinformatics #StructuralBiology
VS Code: set dictionary path in settings
Python script: pass dictionary path via CLI
#mmCIF #PDB #Bioinformatics #StructuralBiology
New Title Alert: vossvolvox- a C++17 command-line tools for analyzing molecular structures, specifically for computing volumes, channels, cavities, and tunnel geometry from various molecular input formats.
Learn more here: buff.ly/0ff33pF
#SBGrid #SBGridSoftware
Learn more here: buff.ly/0ff33pF
#SBGrid #SBGridSoftware
GitHub - vosslab/vossvolvox: This repository provides C++17 command-line tools for analyzing molecular structures by computing volumes, channels, cavities, and tunnel geometry from PDB, mmCIF, PDBML, or XYZR inputs. It is intended for researchers in structural biology and molecular biophysics who need reproducible grid-based analyses.
This repository provides C++17 command-line tools for analyzing molecular structures by computing volumes, channels, cavities, and tunnel geometry from PDB, mmCIF, PDBML, or XYZR inputs. It is inte...
buff.ly
March 26, 2026 at 4:04 PM
New Title Alert: vossvolvox- a C++17 command-line tools for analyzing molecular structures, specifically for computing volumes, channels, cavities, and tunnel geometry from various molecular input formats.
Learn more here: buff.ly/0ff33pF
#SBGrid #SBGridSoftware
Learn more here: buff.ly/0ff33pF
#SBGrid #SBGridSoftware
It is probably only useful to me, but just in case I have put it on github - caveat emptor, I have not tested it extensively, but it seems to give sensible results. I just like to have an annotated sequence handy while building, and this scratches that itch. (3/3) github.com/olibclarke/p...
GitHub - olibclarke/protein_sequence_annotator: Quick script to generate a secondary structure and pLDDT annotated sequence figure from a PDB/mmCIF
Quick script to generate a secondary structure and pLDDT annotated sequence figure from a PDB/mmCIF - olibclarke/protein_sequence_annotator
github.com
March 19, 2026 at 11:10 PM
It is probably only useful to me, but just in case I have put it on github - caveat emptor, I have not tested it extensively, but it seems to give sensible results. I just like to have an annotated sequence handy while building, and this scratches that itch. (3/3) github.com/olibclarke/p...
So I thought I'd make a quick semi-replacement (a python script using gemmi & mkdssp, mostly written with Codex).
It just takes the PDB/mmcif & plots the sequence, with secondary structure from mkdssp, and colors the secondary structure by pLDDT or B-factor. (2/3)
It just takes the PDB/mmcif & plots the sequence, with secondary structure from mkdssp, and colors the secondary structure by pLDDT or B-factor. (2/3)
March 19, 2026 at 11:10 PM
So I thought I'd make a quick semi-replacement (a python script using gemmi & mkdssp, mostly written with Codex).
It just takes the PDB/mmcif & plots the sequence, with secondary structure from mkdssp, and colors the secondary structure by pLDDT or B-factor. (2/3)
It just takes the PDB/mmcif & plots the sequence, with secondary structure from mkdssp, and colors the secondary structure by pLDDT or B-factor. (2/3)
𝗣𝗗𝗕𝗲 𝗺𝗺𝗖𝗜𝗙 𝗩𝗮𝗹𝗶𝗱𝗮𝘁𝗼𝗿: validate your mmCIF files against PDBx/mmCIF dictionary
✅ Real-time check
✅ Metadata completeness indicator
pip install pdbe-mmcif-validator
install VS code extension: marketplace.visualstudio.com/items?itemNa...
GitHub - PDBeurope/mmcif-validator: github.com/PDBeurope/mm...
✅ Real-time check
✅ Metadata completeness indicator
pip install pdbe-mmcif-validator
install VS code extension: marketplace.visualstudio.com/items?itemNa...
GitHub - PDBeurope/mmcif-validator: github.com/PDBeurope/mm...
March 18, 2026 at 11:26 AM
𝗣𝗗𝗕𝗲 𝗺𝗺𝗖𝗜𝗙 𝗩𝗮𝗹𝗶𝗱𝗮𝘁𝗼𝗿: validate your mmCIF files against PDBx/mmCIF dictionary
✅ Real-time check
✅ Metadata completeness indicator
pip install pdbe-mmcif-validator
install VS code extension: marketplace.visualstudio.com/items?itemNa...
GitHub - PDBeurope/mmcif-validator: github.com/PDBeurope/mm...
✅ Real-time check
✅ Metadata completeness indicator
pip install pdbe-mmcif-validator
install VS code extension: marketplace.visualstudio.com/items?itemNa...
GitHub - PDBeurope/mmcif-validator: github.com/PDBeurope/mm...