Jochem Smit

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)

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

@marimo_io finally, I found @Jhsmit_ developped the ipymolstar which worked well with marimo.

We wrote a step-by-step tutorial how transform a GitHub repository of notebooks into a collection of interactive data apps 🚀 marimo.io/blog/github-no…

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/sh…

Code available on @py_cafe: py.cafe/jhsmit/ipymols… 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

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)

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!

There is a live example on @py_cafe: app.py.cafe/jhsmit/ipymols…

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

@Panel_org Thanks! Something like this: github.com/Jhsmit/ipymols…? it doesnt work yet but I think its because of how I import in js

FYI @Jhsmit_. Maybe that would be useful for the chemistry component you maintain?

2 for the price of 1. You can now create widgets for both @ProjectJupyter and @Panel_org using the same #AnyWidget Javascript code. 🧵👇Check out the tutorials below. #python #dataviz #datascience #Analytics

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/tetrame…

forgot step 3. share the link: 😅 py.cafe/jhsmit/ipymols…

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 😎

@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: py.cafe/jhsmit/dimeriz…

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 🧵👇🏻

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

link to huggingface space: huggingface.co/spaces/Jhsmit/… With PDBeMolstar 0.3.2 / ipymolstar 0.0.5 you can also set custom tooltips. Neat!

#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.

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

@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. pypi.org/project/molvie…

@Jhsmit_ @molstar0 Fantastic!! Wishing you much success with your project - I'm very interested in making the Mol* tech stack accessible/interact-with-able (outside of molecular vis) from Python and psyched to see someone pushing this 🥰

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

@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: github.com/Jhsmit/ploombe… I'm planning to add hover/click callbacks

@Jhsmit_ This is wonderful - interacting with the visualisation from Python should be possible with the two way data binding provided by anywidget, have you explored this kind of functionality? MolQL from @molstar0 may be useful here I’m thinking selection and coloring, animation… 😍

@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: github.com/Jhsmit/ploombe…

@Jhsmit_ This is wonderful, thank you. Is it possible to load from a URL (a non PDB URL?)