Joined December 2012
- Tweets 255
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32 Photos and videos
Pinned Tweet
4 Nov 2024
New feature in #ipymolstar v0.0.7: You can now use the mouseover event to highlight protein residues bidirectionally between #altair charts.
In this example the colors represent PyHDX derived #hdxms ΔG's (roughly local flexibility)
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Jochem Smit retweeted
5 Nov 2024
FRET correlation functions, a new model-free analysis tool. For dynamics from nano to milliseconds in diffusion-based smFRET experiments. Clean correlation functions, no diffusion component left. Perfect to verify HMM fits. biorxiv.org/cgi/content/shor…
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4 Nov 2024
New feature in #ipymolstar v0.0.7: You can now use the mouseover event to highlight protein residues bidirectionally between #altair charts.
In this example the colors represent PyHDX derived #hdxms ΔG's (roughly local flexibility)
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4 Nov 2024
Code available on @py_cafe: py.cafe/jhsmit/ipymolstar-al…
This is using altair's JupyterChart which works really well if you want to get selections with python. You can't set selections yet, so I'm 'manually' setting the x-pos of the line. Is there a better way?
#anywidget @vega_vis
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Jochem Smit retweeted
31 Oct 2024
Just out in time for Michele's viva tomorrow - his Magnum Opus (what a 4 month progress report can turn into!). Anything you ever didn't care to ask about HDX software is here - well almost 🙂 And good luck tomorrow morning for x-less Michele!
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8 Oct 2024
You can now use ipymolstar in panel apps 🥳
ipymolstar v0.0.6 adds panel's AnyWidgetComponent so you can interact with the PDBeMolstar widget directly from panel/python🐍
@Panel_org @MarcSkovMadsen @PhilippJFR
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13 Jun 2024
By popular demand: How much monomer/dimer/tetramer are formed at steady-state given the two kds and the total concentration of protomer? 🧐
py.cafe/jhsmit/tetramerizati…
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11 Jun 2024
Here is another fun one over on @py_cafe ☕️
Protein residue coloring in ipymolstar is now super fast with the latest PDBeMolstar version.
Makes for very responsive protein viewer apps!
And supports dark mode 😎
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Jochem Smit retweeted
11 Jun 2024
Super excited to announce the pre-release of @py_cafe 🎉
py.cafe is a platform that lets you create, run, edit, and share Python (web) applications directly in your browser. No installation is needed—just a single click, and it runs!
#Python #pyodide
🧵👇🏻
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Jochem Smit retweeted
We have several positions open in our lab ! 📢🥳
Check our tweet feed !
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13 May 2024
#alphafold3 is incredible!
I've created this #solara app where you can drag & drop your result .zip file and switch between chain color or plddt colors. Includes 'spin' and theme toggle for maximal viewing pleasure.
The video below shows the elusive SecA2/SecB4 complex.
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13 May 2024
link to huggingface space: huggingface.co/spaces/Jhsmit…
With PDBeMolstar 0.3.2 / ipymolstar 0.0.5 you can also set custom tooltips. Neat!
ALT screenshot of ipymolstar viewer with custom tooltip
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Jochem Smit retweeted
29 Apr 2024
AnyWidget Solara: How to build a basic widget with AnyWidget by @trevmanz in a Solara @solara_dev app
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25 Apr 2024
New in #ipymolstar version 0.0.4: directly load your local data files
`pip install "ipymolstar==0.0.4"`
github.com/Jhsmit/ipymolstar
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Jochem Smit retweeted
16 Apr 2024
OPIG Postdoc Olly Crook (@OllyMCrook) has released the RexMS package for residue-level analysis of hydrogen deuterium exchange mass spectrometry (HDX-MS) data.
Read the preprint here: biorxiv.org/content/10.1101/…
And explore the codebase here:
ococrook.github.io/RexMS/
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18 Mar 2024
I've created my first widget with #anywidget! Its called `ipymolstar` and allows visualization of proteins or molecules interactively from python
check out the video below where I'm using ipymolstar in a @solara_dev app
or try the live demo on ploomber: purple-glade-1760.ploomberap…
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18 Mar 2024
ipymolstar uses Mol* via the PDBeMolstar implementation.
Current release is v0.0.3 where most basic functionality is implemented. Mouseover events from js to python are next on the list!
@maartenbreddels @trevmanz @asrmoin @ploomber
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18 Mar 2024
.. and dark mode is also supported!
ALT screenshot of ipymolstar solara app in dark mode
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Jochem Smit retweeted
18 Sep 2023
Also, if you want a fancy movie of the predicted states of your protein fold, i adapted the ColabFold implementation of ESMFold to do this in this notebook. Also #ChimeraX is needed
colab.research.google.com/dr…
Here are 3 examples with distincts folds. This is the Top7 fold :)
18 Sep 2023
"Rendering protein mutation movies with MutAmore"
(gif below made from youtube.com/watch?v=1XgiFXg-…)
biorxiv.org/content/10.1101/…
github.com/kWeissenow/MutAmo…
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