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asrose.bsky.social
Alexander Rose
@asrose.bsky.social
560 followers 560 following 16 posts
Scientific software engineer & computational structural biologist, #molstar web molecular graphics developer.
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · 5d
#molstar now supports immersive AR/VR - enjoy

molstar.org/xr/
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · 2d
Congrats to the 2025 #NobelPrize laureates in chemistry.

Here are some #molstar renderings of an AgFe mixed metal Metal Organic Framework to celebrate.
asrose.bsky.social
Alexander Rose @asrose.bsky.social · 4d
😂
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · 5d
#molstar now supports immersive AR/VR - enjoy

molstar.org/xr/
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Reposted by Alexander Rose
rcsbpdb.bsky.social
RCSB Protein Data Bank @rcsbpdb.bsky.social · 11d
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
2 7
Reposted by Alexander Rose
rcsbpdb.bsky.social
RCSB Protein Data Bank @rcsbpdb.bsky.social · 16d
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
4 15
Reposted by Alexander Rose
rcsbpdb.bsky.social
RCSB Protein Data Bank @rcsbpdb.bsky.social · Aug 5
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
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Reposted by Alexander Rose
jhsmit.bsky.social
Jochem Smit @jhsmit.bsky.social · Apr 10
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/
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Reposted by Alexander Rose
joachim123.bsky.social
Joachim Frank @joachim123.bsky.social · Mar 17
sorry, trying better res
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Jan 18
Isosurface of X-ray density only lit by emissive slice of same density. Illuminated in #molstar.
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Reposted by Alexander Rose
jhsmit.bsky.social
Jochem Smit @jhsmit.bsky.social · Dec 6
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
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Reposted by Alexander Rose
jhsmit.bsky.social
Jochem Smit @jhsmit.bsky.social · Dec 6
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.
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Reposted by Alexander Rose
bradyajohnston.bsky.social
Brady Johnston @bradyajohnston.bsky.social · Dec 1
A quick molecule of the month render for November's Malaria Parasite PTEX (pdb101.rcsb.org/motm/299) using #b3d and #MolecularNodes

#GeometryNodes #SciArt
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Reposted by Alexander Rose
jhsmit.bsky.social
Jochem Smit @jhsmit.bsky.social · Nov 29
#ipymolstar v0.0.9: Added click interactions

try it on pycafé: py.cafe/jhsmit/ipymo...
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 23
Splendid, thank you
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
Try Mol* illumination mode: molstar.org/viewer/?illu...

Example: molstar.org/viewer/?snap...
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
A few notes on integrating SSGI into Mol*.
Integration Progressive rendering Keep viewport interactive Use requestAnimationFrame Also check `gl.SYNC_GPU_COMMANDS_COMPLETE` if available Because requestAnimationFrame may fire even if GPU is still busy Adjust quality parameters based on previous iterations’ render time Adjust denoise threshold to hide graininess So instead of grainy to non-grainy it goes from blurry to non-blurry Screenshots Browsers may lose the WebGL context if render time of a single frame is too large or too many frames are submitted to the GPU Check `gl.SYNC_GPU_COMMANDS_COMPLETE` if available, otherwise use `gl.readPixels` to wait Anti-aliasing Since normals and direct-light are pre-calculated, jittering rays is not enough Recalculate normals and direct light with jittered camera, trace and blend
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
For tracing in screen-space we need to recover thickness.
Want it automatic, not fiddle with parameters.

Insight: Molecules are shown with visuals of very different density.

So we do 2 things
1) Base thickness from front- and back-face depth
2) Density factor to adjust for each type of visual
Thickness For tracing in screen-space we need to estimate the thickness Automatic thickness (estimate) Base thickness as max(backface depth) - min(frontface depth) Per object density factor to adjust base thickness Fixed thickness Want to avoid as we have representations with different “densities” Still support in-case user wants to do manual tweaks
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
Inputs are rendered by the same shader code as the standard rendering. There are just two extra output targets: normal + emissive strength and diffuse + density. Additionally we do a pass to get back face depth.
Tracing Inputs Shaded color (rgba, standard pass) Normal (xyz) + emissive strength (w) Diffuse color (rgb) + “density” (a) Front depth Back depth Sampling Backwards Monte Carlo Only diffuse (“specular” from shaded input) Russian Roulette to boost non-terminated rays Tracing Hit background Return background color Hit surface, then nothing Return shaded color Hit surface, bounce x times, then nothing Return shaded color plus accumulated diffuse of bounces Hit surface, bounce more than x times Return no color
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
Main idea is to treat the SSGI as a progressive enhancement of sorts. Try to reuse as many of the passes used for normal rendering. And keep the overall look as similar as possible.
Passes On change (camera, geometry, lighting, …) Transparent geometry pass Post-processing input passes (outline, marking, transparent ssao) Tracing input pass Backface depth pass Sampling Tracing sample pass Compose Compose pass (denoise, blend transparent geometry, apply outlines, transparent ssao) Background pass Antialiasing pass Bloom pass DoF pass
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
High quality lighting from "path-traced" screen-space global illumination. Even works with only emissive lights.
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 17
Gave a short presentation on Illuminating Molecules in #molstar at the November 2024 #WebGL & #WebGPU Meetup

www.khronos.org/events/webgl...
About Mol* Suite of tools for 3D molecular data on the web Custom WebGL rendering engine Scales from single atoms to cells with billions Wanted nicer lighting that still scales “Path-traced” SSGI Screen-space, so OK with billions of atoms Sample-based, so good to adjust quality
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 16
How long does the denoiser take compared to the rest?
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asrose.bsky.social
Alexander Rose @asrose.bsky.social · Nov 16
Hard to judge detail quality but looks so smooth, very nice.
Reposted by Alexander Rose
briankaris.bsky.social
Brian Karis @briankaris.bsky.social · Nov 15
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
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Reposted by Alexander Rose
rborza.bsky.social
Razvan Borza @rborza.bsky.social · Oct 28
🚀 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...
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