Alexander Rose
@asrose.bsky.social
Scientific software engineer & computational structural biologist, #molstar web molecular graphics developer.
Pinned
Congrats to the 2025 #NobelPrize laureates in chemistry.
Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.
Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.
October 8, 2025 at 5:06 PM
Congrats to the 2025 #NobelPrize laureates in chemistry.
Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.
Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.
October 6, 2025 at 1:06 AM
Reposted by Alexander Rose
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 (
www.youtube.com
September 29, 2025 at 4:33 PM
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
Reposted by Alexander Rose
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
September 24, 2025 at 4:12 PM
MolViewSpec: describe, share, and reproduce Mol* molecular scenes with a simple extension
Reposted by Alexander Rose
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...
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
August 5, 2025 at 4:12 PM
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...
Learn how to align one or more protein chains to a reference structure in a pairwise manner
pdb101.rcsb.org/news...
Reposted by Alexander Rose
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/
ipymolstar repo: github.com/jhsmit/ipymo...
Molviewspec: molstar.org/mol-view-spec/
April 10, 2025 at 10:24 AM
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/
ipymolstar repo: github.com/jhsmit/ipymo...
Molviewspec: molstar.org/mol-view-spec/
Reposted by Alexander Rose
sorry, trying better res
March 17, 2025 at 12:25 AM
sorry, trying better res
Reposted by Alexander Rose
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)
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
December 6, 2024 at 3:17 PM
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)
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)
Reposted by Alexander Rose
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.
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.
December 6, 2024 at 3:17 PM
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.
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.
Reposted by Alexander Rose
A quick molecule of the month render for November's Malaria Parasite PTEX (pdb101.rcsb.org/motm/299) using #b3d and #MolecularNodes
#GeometryNodes #SciArt
#GeometryNodes #SciArt
December 1, 2024 at 5:52 AM
A quick molecule of the month render for November's Malaria Parasite PTEX (pdb101.rcsb.org/motm/299) using #b3d and #MolecularNodes
#GeometryNodes #SciArt
#GeometryNodes #SciArt
Reposted by Alexander Rose
November 29, 2024 at 4:58 PM
Gave a short presentation on Illuminating Molecules in #molstar at the November 2024 #WebGL & #WebGPU Meetup
www.khronos.org/events/webgl...
www.khronos.org/events/webgl...
November 17, 2024 at 9:47 PM
Gave a short presentation on Illuminating Molecules in #molstar at the November 2024 #WebGL & #WebGPU Meetup
www.khronos.org/events/webgl...
www.khronos.org/events/webgl...
Reposted by Alexander Rose
Significant new work on LOD of aggregates! mangosister.github.io/scene_agn_si...
Efficient Scene Appearance Aggregation for Level-of-Detail Rendering
mangosister.github.io
November 15, 2024 at 6:19 PM
Significant new work on LOD of aggregates! mangosister.github.io/scene_agn_si...
Reposted by Alexander Rose
🚀 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...
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...
October 28, 2024 at 7:03 PM
🚀 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...
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...
Reposted by Alexander Rose
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
November 8, 2024 at 7:20 AM
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)
Reposted by Alexander Rose
Two-way tertiary/primary structure hover and highlight with #ipymolstar and #altair
Try it on pycafe: py.cafe/jhsmit/ipymo...
Try it on pycafe: py.cafe/jhsmit/ipymo...
November 7, 2024 at 3:21 PM
Two-way tertiary/primary structure hover and highlight with #ipymolstar and #altair
Try it on pycafe: py.cafe/jhsmit/ipymo...
Try it on pycafe: py.cafe/jhsmit/ipymo...