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.

Beautiful and technically impressive work. Nice to see it highlighted.

Tim Davison ᯅ@timd-ca.bsky.social · last mo.

Apple shared CellWalk's story today, which began with David Goodsell's The Machinery of Life. Grateful to the people at Apple who worked on this :) developer.apple.com/news/?id=7qd...

Excited to share this paper from @yiechanglin.bsky.social showing how lipids can move between bacterial membranes along the bridge like protein TamB. Also happy to be able to post the cool movie. 🎥🌟 #MDsimulations #StructuralBiology doi.org/10.1016/j.bp...

Try this new online training game from Leandro F. Estrozi designed for newcomers in structural biology, with a focus on cryo-EM and cryo-ET map interpretation: rico.ibs.fr/helixplo...

Explore PDB Structures in AR/VR RCSB PDB supports immersive Augmented Reality and Virtual Reality (VR) visualization within Mol*

Explore PDB Structures in AR/VR

RCSB.org supports immersive Augmented Reality and Virtual Reality (VR) visualization within Mol*

rcsb.org

Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578

🚨New pre-print!🚨 Because influenza virions are highly variable in form no single method can show their molecular architecture in detail. Here, we integrate multiple structural and compositional approaches to identify new features of these beautiful virus particles www.biorxiv.org/content/10.6...

latest #molstar publication pulling all details on its graphics engine together - lots of pretty pictures with Gianluca Tomasello (@proteinimaging.bsky.social), Áron Samuel Kovács, @ludovicautin.bsky.social, David Sehnal pmc.ncbi.nlm.nih.gov/articles/PMC...

Mol* Web Molecular Graphics Engine

Web-based molecular graphics have transformed the interactive visualization of molecular data, leveraging modern web technologies that provide GPU acceleration, optimized JavaScript engines, and seamless access across devices without additional ...

pmc.ncbi.nlm.nih.gov

Trying some procedural animation for #molstar. Not real in any sense but intended to convey dynamics. github.com/molstar/mols...

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

Register for this January 26 webinar to learn what is new in the redesigned Advanced Search feature and how to use it go.rutgers.edu/ijwpxr1h

Congrats to the 2025 #NobelPrize laureates in chemistry. Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.

#molstar now supports immersive AR/VR - enjoy molstar.org/xr/

Watch the Pairwise Alignment Tool Office Hour and learn how to align one or more protein chains to a reference structure in a pairwise manner

Introduction to RCSB PDB’s Pairwise Alignment Tool

The Pairwise Structure Alignment Tool (https://www.rcsb.org/alignment) can align one or more protein chains to a reference structure in a pairwise manner. This tool allows for simultaneous analysis and visualization of three-dimensional (3D) structure alignments and structure-based one-dimensional (

youtube.com

MolViewSpec: describe, share, and reproduce Mol* molecular scenes with a simple extension

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations

Abstract. Data visualization is a pivotal component of a structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broade

academic.oup.com

Register for the Aug 11 Virtual Office Hour on Pairwise Alignment Learn how to align one or more protein chains to a reference structure in a pairwise manner pdb101.rcsb.org/news...

PDB101: Register for the Aug 11 Virtual Office Hour on Pairwise Alignment

PDB-101: Training, Outreach, and Education portal of RCSB PDB

pdb101.rcsb.org

New release for #ipymolstar: I've added a widget for the amazing and very powerful MolViewSpec. This allows you to control the camera📷from python🐍, as well as all other molviewspec features 🎉 ipymolstar repo: github.com/jhsmit/ipymo... Molviewspec: molstar.org/mol-view-spec/

sorry, trying better res

Isosurface of X-ray density only lit by emissive slice of same density. Illuminated in #molstar.

You can try it on Huggingface: huggingface.co/spaces/Jhsmi... The data is only encoded in the link and not stored so you can use it to share unpublished data* (at your own risk, no warranty, links might stop working)

Ipymolstar Annotate Colors - a Hugging Face Space by Jhsmit

Annotate protein structural models with colors

huggingface.co

Here's a neat way to share you protein-annotated data 🚀🧪 Upload your .csv with residue/value data, select data column, colormap and norm to interactively color your protein model. Then, add title/description and click the button to open a shareable view with url-encoded data and settings.

A quick molecule of the month render for November's Malaria Parasite PTEX (pdb101.rcsb.org/motm/299) using #b3d and #MolecularNodes #GeometryNodes #SciArt

#ipymolstar v0.0.9: Added click interactions try it on pycafé: py.cafe/jhsmit/ipymo...

Gave a short presentation on Illuminating Molecules in #molstar at the November 2024 #WebGL & #WebGPU Meetup www.khronos.org/events/webgl...

Significant new work on LOD of aggregates! mangosister.github.io/scene_agn_si...

🚀 Excited about our pre-print: AlphaBridge: A User-Friendly Tool for Interpreting Protein Predictions Whether you're an expert or just new to the field of Protein Prediction, AlphaBridge is the way to go! 🔁Try it and share your thoughts! 📜 Article: www.biorxiv.org/content/10.1...

InterProt (interprot.com#/sae-viz/SAE...) is a tool that applies the same interpretability analysis used to make Golden Gate Claude to protein language models. For example feature 4000 recognizes residues lining inside of de novo designed & natural transmembrane beta-barrels (PDBs 6X1K, 6X9Z, 2MLH)

InterProt

Interpreting Proteins through Language Models

interprot.com

Two-way tertiary/primary structure hover and highlight with #ipymolstar and #altair Try it on pycafe: py.cafe/jhsmit/ipymo...

Ionic lock in inactive rhodopsin - illuminated in #molstar