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...
Changes in PDB IDs are coming that will require use of PDBx/mmCIF file format... will you be ready? #MayThe4th
Resources are available to help: www.wwpdb.org/docume...
Resources are available to help: www.wwpdb.org/docume...
May 4, 2025 at 4:12 PM
Changes in PDB IDs are coming that will require use of PDBx/mmCIF file format... will you be ready? #MayThe4th
Resources are available to help: www.wwpdb.org/docume...
Resources are available to help: www.wwpdb.org/docume...
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.
New Title Alert: PDBImages- a command-line tool from PDBe EMBL-EBI for generating images of macromolecular structures from mmCIF or binary CIF structure files based on Mol*.
Learn more here: https://buff.ly/3DL7ZKJ
#SBGrid #Software #StructuralBiology
Learn more here: https://buff.ly/3DL7ZKJ
#SBGrid #Software #StructuralBiology
GitHub - PDBeurope/pdb-images: Generates images from mmCIF/BCIF files
Generates images from mmCIF/BCIF files. Contribute to PDBeurope/pdb-images development by creating an account on GitHub.
buff.ly
February 25, 2025 at 12:00 PM
New Title Alert: PDBImages- a command-line tool from PDBe EMBL-EBI for generating images of macromolecular structures from mmCIF or binary CIF structure files based on Mol*.
Learn more here: https://buff.ly/3DL7ZKJ
#SBGrid #Software #StructuralBiology
Learn more here: https://buff.ly/3DL7ZKJ
#SBGrid #Software #StructuralBiology
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
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...
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 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?
I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...
pip install ipsae
from www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...
from www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...
Screen binders using ipSAE
YouTube video by ProteinDesignStudio
www.youtube.com
January 3, 2026 at 11:06 AM
I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...
🧬 Exciting AlphaFold DB updates:
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
March 4, 2025 at 6:18 PM
🧬 Exciting AlphaFold DB updates:
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
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...
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:
mmCIF Rainbow Columns (VS Code Extension)
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
Rainbow mmCIF - Visual Studio Marketplace
Extension for Visual Studio Code - Column-based coloring for mmCIF loops.
marketplace.visualstudio.com
December 26, 2025 at 2:46 AM
mmCIF Rainbow Columns (VS Code Extension)
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
marketplace.visualstudio.com/items?itemNa...
It is designed to make reading and editing complex loop_ blocks easier. Unlike existing CIF editors or syntax highlighters, this extension focuses on human-readable visualization of mmCIF loop columns.
🚨 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
🚨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
@jeremywohlwend.bsky.social
@gcorso.bsky.social
Can you guys check on post-translationally modified amino acids in proteins in Boltz-1?
This model has a backbone O and OXT for an internal TPO. There should only be an OXT if it s C-terminal residue.
Also, mmcif seq is (ALA)(SER) instead of AS...
@gcorso.bsky.social
Can you guys check on post-translationally modified amino acids in proteins in Boltz-1?
This model has a backbone O and OXT for an internal TPO. There should only be an OXT if it s C-terminal residue.
Also, mmcif seq is (ALA)(SER) instead of AS...
March 1, 2025 at 8:06 AM
@jeremywohlwend.bsky.social
@gcorso.bsky.social
Can you guys check on post-translationally modified amino acids in proteins in Boltz-1?
This model has a backbone O and OXT for an internal TPO. There should only be an OXT if it s C-terminal residue.
Also, mmcif seq is (ALA)(SER) instead of AS...
@gcorso.bsky.social
Can you guys check on post-translationally modified amino acids in proteins in Boltz-1?
This model has a backbone O and OXT for an internal TPO. There should only be an OXT if it s C-terminal residue.
Also, mmcif seq is (ALA)(SER) instead of AS...
🚨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
New release of BioStructures.jl just out: github.com/BioJulia/Bio....
Featuring chi angle calculation, mmCIF secondary structure reading and bonded graph construction all thanks to Tim Holy.
Featuring chi angle calculation, mmCIF secondary structure reading and bonded graph construction all thanks to Tim Holy.
GitHub - BioJulia/BioStructures.jl: A Julia package to read, write and manipulate macromolecular structures
A Julia package to read, write and manipulate macromolecular structures - BioJulia/BioStructures.jl
github.com
May 12, 2025 at 9:50 AM
New release of BioStructures.jl just out: github.com/BioJulia/Bio....
Featuring chi angle calculation, mmCIF secondary structure reading and bonded graph construction all thanks to Tim Holy.
Featuring chi angle calculation, mmCIF secondary structure reading and bonded graph construction all thanks to Tim Holy.
wwPDB community: Take the PDBx/mmCIF User Guide Survey.
Respondents can enter a drawing for a chance to win a prize from the wwPDB.
rutgers.ca1.qualtric...
Respondents can enter a drawing for a chance to win a prize from the wwPDB.
rutgers.ca1.qualtric...
PDBx/mmCIF User Guide Survey
PDBx/mmCIF User Guide Survey
rutgers.ca1.qualtrics.com
January 28, 2025 at 5:12 PM
wwPDB community: Take the PDBx/mmCIF User Guide Survey.
Respondents can enter a drawing for a chance to win a prize from the wwPDB.
rutgers.ca1.qualtric...
Respondents can enter a drawing for a chance to win a prize from the wwPDB.
rutgers.ca1.qualtric...
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/
ICYMI: PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats
First 5-character ligand has been released: www.rcsb.org/ligand/...
Details: www.wwpdb.org/news/n...
First 5-character ligand has been released: www.rcsb.org/ligand/...
Details: www.wwpdb.org/news/n...
January 3, 2024 at 9:32 PM
ICYMI: PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats
First 5-character ligand has been released: www.rcsb.org/ligand/...
Details: www.wwpdb.org/news/n...
First 5-character ligand has been released: www.rcsb.org/ligand/...
Details: www.wwpdb.org/news/n...
If you read this far, you get the Code: github.com/DunbrackLab/... . Runs on AF2, AF3-server, and AF3-local json files and their pdb/mmCIF files. No special flags. MIT license. Let me know of any bugs or questions. End 🧵.
GitHub - DunbrackLab/IPSAE: Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3
Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3 - DunbrackLab/IPSAE
github.com
February 16, 2025 at 2:13 AM
If you read this far, you get the Code: github.com/DunbrackLab/... . Runs on AF2, AF3-server, and AF3-local json files and their pdb/mmCIF files. No special flags. MIT license. Let me know of any bugs or questions. End 🧵.
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