I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!
cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircosconta... […]
🧬 Testing beta-lactamase resistance with AlphaFold + DiffDock + GROMACS! Watch clavulanic acid bind TEM-5, CTX-M-15, KPC-2, and get rejected by TEM-30. Simulation confirms biology! 🔬💊 #gromacs #diffdock #chimerax #moleculardynamic #alphafold
Ever wanted to hold a cilium in your hand? 🧬✨
Here is a look at how I’m using CiliaBuilder in @UCSFChimeraX to generate accurate 3D prints of centrioles and cilia. Perfect for teaching or lab displays!
Watch the process: youtu.be/IKnnp3ovptQ #CryoEM #CellBio #ChimeraX
📋 Requisitos:
✅ Inscripción previa (gratuita): forms.gle/GejEqSyVxkUL...
💻 Ordenador portátil
🔗 Cuenta Google activa + instalación previa de #ChimeraX (cgl.ucsf.edu/chimerax/dow...)
🌟 ¡Y muchas ganas de aprender!
Plazas limitadas — ¡reserva tu lugar hoy mismo!
Durante el workshop aprenderás a:
🔹 Analizar estructuras de proteínas con #ChimeraX
🔹 Predecir modelos con #AlphaFold3
🔹 Diseñar proteínas artificiales (de novo protein binders)
🔹 Entender cómo la #IA transforma la biología estructural
As invited, someone indeed came to our booth to see his own lipase #protein #structure project in #HoloDeck - fantastic! We prepared the file within a few minutes using #UCSF #ChimeraX & presented it in #AugmentedReality.
#DIYbio #lab #instruments #bioinformatics #CompChem #AR #education #STEM #MINT
Had a great chat about the historical breakthroughs in #cryoEM with Basile Wicky: plunge freezing, direct electron detectors, algorithms. But I forgot to mention one: we owe a lot to soft light rendering in #ChimeraX
How can structural insights refine your research? Join our 2-day course in Ghent (8-9 Sept 2025) on protein structure analysis & prediction. Learn #ChimeraX, #AlphaFold 2/3, #MutateX, and more.
Register by 25 Aug 👉 vibbio.tech/3Ze9goP #StructuralBiology #AlphaFold #VIBTraining
Colour your protein's secondary structure with a gradient in #ChimeraX! I made a script that applies a continuous colour palette available in matplotlib onto any protein with helices or coils.
🧵
Quick tip for busy people: you can improve the aesthetic of your proteins using the following commands in #ChimeraX. You can also add some shadows using the visual effects available in PowerPoint <protein emoji>
ps. before the render, remove the struts using the visual display
Has anyone else had their computer bluescreen from #ChimeraX?
I was having it export to .stl, and that seems to have caused some kind of graphics card failure.
Anyone else have any similar experiences or knowledge of how to avoid this?
#MicroSky, #CryoEM, #StructuralBiology
👋 Re-sharing my first render using #Blender. My interpretation of the vitreous ice on #CryoEM grids.
I think this was pre- #MolecularNodes, so I exported the cryo-EM density from #ChimeraX (?) I remember my macbook struggling with the many protein copies 😅
Makes me want to do more Sci-Vis!
🚨 New #P2Rank release out! P2Rank can now run #fpocket directly and then re-score predictions with PRANK. Additionally, #ChimeraX is now supported for structure visualisation. Glad to have had my tiny contribution to this feature! And it looks so good!
PDB: 4GQQ @pdbeurope.bsky.social
#ChimeraX is just great. It is my favourite viewer and I love making figures with it! Check some of them in our new paper: tinyurl.com/Utges-LBS
In here we illustrate redundancy in test sets, incomplete train sets, redundancy in prediction, protein shape class, pocket shape similarity...
🚀 P2Rank 2.5 now offers #ChimeraX visualizations of ligand-binding site predictions (alongside #PyMOL ones)! Huge thanks to @javierutges.bsky.social and ChimeraX team for inspiration and help.
Release Details: github.com/rdk/p2rank/r...
💡 Feedback welcome!
#Bioinformatics #DrugDiscovery
Just a typical Saturday morning making figures in my car while I wait for my daughter’s acrobatics class to be done 😄
#crystallography #chimeraX #momlife #academicmom
If anyone is wondering where those waters are... I clicked the de-dust button on #chimerax 😳
#ChimeraX is at the bleeding edge of supporting elaborate visualization and structure analysis, together with virtual reality for example, which stands to accelerate discovery, but needs considerable investment to implement and maintain.
https://www.youtube.com/watch?v=dKNbRRRFhqY
Today, tools like #Chimera and #ChimeraX are an essential part of our toolkits when exploring drug targets such as CD20, and terrible conditions as varied as cancers and multiple sclerosis. x.com/AlexisRohou/status/12306...
#UCSF #ChimeraX is just getting so, so good. Favorite new feature: right click on any blob of density and have it colored and measured! https://www.cgl.ucsf.edu/chimerax/
Favorite new feature in #ChimeraX so far: "volume #3-4 toggle" let's you do quick comparisons between maps. For years I wanted this in Chimera!
