Jochem Smit

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

[Jochem Smit @Jhsmit_]

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)

[Jochem Smit @Jhsmit_]

@Biocheming @marimo_io does theme='dark' work in marimo? I'm surprised you get a black background with theme='light'

[Hagen Hofmann 🎗️🇮🇱 @hofmann_hagen]

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. https://t.co/cmzNuNQQn8

[Jochem Smit @Jhsmit_]

Code available on @py_cafe: https://t.co/Qo353OI1se

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

[Jochem Smit @Jhsmit_]

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)

[Frank Sobott @FrankSobott]

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!

[Jochem Smit @Jhsmit_]

There is a live example on @py_cafe:

https://t.co/CLDK5r2syJ

[Jochem Smit @Jhsmit_]

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

[Jochem Smit @Jhsmit_]

@Panel_org Thanks!
Something like this: https://t.co/TlSyCPPzx5?

it doesnt work yet but I think its because of how I import in js

[Jochem Smit @Jhsmit_]

By popular demand: How much monomer/dimer/tetramer are formed at steady-state given the two kds and the total concentration of protomer? 🧐

https://t.co/gSY31dJvBF

[Jochem Smit @Jhsmit_]

forgot step 3. share the link: 😅
https://t.co/4U8skRs3xU

[Jochem Smit @Jhsmit_]

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 😎

[Jochem Smit @Jhsmit_]

@maartenbreddels @py_cafe sharing = caring 😃

@py_cafe makes it super easy to share small apps with my lab mates

Here is doing something we deal with a lot: calculate monomer-dimer steady state kinetics

All i have to do is paste in the code and share the link:
https://t.co/QyAn3SreCx

[Maarten A. Breddels @maartenbreddels]

Super excited to announce the pre-release of @py_cafe 🎉

https://t.co/XybqBunNyn 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
🧵👇🏻

[Dedecker Lab (dedeckerlab.bsky.social) @DedeckerLab]

We have several positions open in our lab ! 📢🥳
Check our tweet feed !

[Jochem Smit @Jhsmit_]

link to huggingface space: https://t.co/bQluDZIylm

With PDBeMolstar 0.3.2 / ipymolstar 0.0.5 you can also set custom tooltips. Neat!

[Jochem Smit @Jhsmit_]

#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.

[Alonso Silva @alonsosilva]

AnyWidget+Solara: How to build a basic widget with AnyWidget by @trevmanz in a Solara @solara_dev app

[Jochem Smit @Jhsmit_]

@AlisterBurt @molstar0 Thanks!

Have you also seen mol-view-spec? I haven't tried it yet but looks quite powerful. Can be used from python as well, not sure how interactive you can make it, I think only one-way.

https://t.co/6WPzHSvmv4

[Jochem Smit @Jhsmit_]

New in #ipymolstar version 0.0.4: directly load your local data files

`pip install "ipymolstar==0.0.4"`
https://t.co/AsJiQLY8Vi

[Jochem Smit @Jhsmit_]

@AlisterBurt @molstar0 yes indeed !

ipymolstar is based on anywidget, and uses the PDBEmolstar implementation, selection/coloring is already added.

There is a demo of this within a #solara app here: https://t.co/IT0UvDeRA2

I'm planning to add hover/click callbacks

[Jochem Smit @Jhsmit_]

@drchristhorpe yes, its possible. I need to work on the ipymolstar documentation, but the PDBeMolstar docs might also help. Links are in ipymolstar github page

Meanwhile there is example code at the solara demo app: https://t.co/IT0UvDeRA2