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Jochem Smit

@jhsmit.bsky.social

125 followers 164 following 26 posts

Biophysics; protein dynamics/folding using smFRET and HDX-MS. jhsmit.org

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Jochem Smit @jhsmit.bsky.social · 16/07/2025

Just updated my hikemap with our Ardennes hikes!🗺️🥾 One of the perks of living in Belgium: epic trails basically in your backyard 🇧🇪🌳 There are a couple of cool two-day hikes here as well which were (rather painful😅) training sessions for our Norway adventure 🇳🇴🏔️ jhsmit.org/hikes/hikema... #hiking

Map of hiking routes in the Belgian Ardennes, with markers and trails highlighting hikes.

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Jochem Smit @jhsmit.bsky.social · 20/05/2025

Such a pleasure to define HDX-MS states directly in VS code! #solara #hdxms-datasets

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Jochem Smit @jhsmit.bsky.social · 17/05/2025

Here in sunny Belgium the tomatos are doing really well this year - they are facing south on the balcony and I invested in some serious pottery

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Jochem Smit @jhsmit.bsky.social · 29/04/2025

Having some fun with 3DPGA & kingdon (GA library for python) in ipymolstar! Geometric Algebra feels like magic 🪄; I don't understand it but surely its very powerful 💪 Live example on pycafe: py.cafe/jhsmit/ipymo...

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Jochem Smit @jhsmit.bsky.social · 10/04/2025

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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Jochem Smit @jhsmit.bsky.social · 06/01/2025

I have some exciting news to share!! A cute little boy arrived in our lives early december Mom & dad are very tired but happy 😃 birth card illustration by Tintenbaum tintenbaum.com

illustration of a baby boy riding a rhino into the sunset

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Jochem Smit @jhsmit.bsky.social · 06/12/2024

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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Jochem Smit @jhsmit.bsky.social · 29/11/2024

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

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Jochem Smit @jhsmit.bsky.social · 07/11/2024

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

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Jochem Smit @jhsmit.bsky.social · 13/05/2024

I've created this #solara app where you can drag & drop your #alphafold3 .zip file and switch between chain color or plddt colors. Includes 'spin' and theme toggle for maximal viewing pleasure. The screenshot below shows the elusive SecA2/SecB4 complex. huggingface.co/spaces/Jhsmi...

A screenshot of the solarafold result viewer showing SecA2:SecB4 complex with plddt residue colors

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Jochem Smit @jhsmit.bsky.social · 25/04/2024

New in #ipymolstar version 0.0.4: directly load your local data files `pip install "ipymolstar==0.0.4"` github.com/Jhsmit/ipymo...

A screenshot of jupyter lab showing a code cell where a local .bcif file is loaded and passed to `PBDeMolstar`. The output is a 3D render of nCov spike protein.

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Jochem Smit @jhsmit.bsky.social · 08/03/2024

Nice! I've updated the structure reference in our HDX-MS database, here it is rendered in ipymolstar (beta) and colored by HDX-MS Gibbs free energy (blue = rigid, yellow = more flexible)

Render of MBP cryoEM structure in ipymolstar with residues coloured by HDX-MS gibbs free energies

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