Brady Johnston
@bradyajohnston
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structural biologist, scientific animator, creator of #MolecularNodes , he/him #rstats #b3d mstd: bradyajohnston @aus .social bsky: @bradyajohnston .bsky.social
Perth, Western Australia
Joined June 2011
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Pinned Tweet
protein motor go brrrrrrrr
Spent the morning sipping my coffee praying that I had enough RAM to import this monster of a structure into blender. (with success)
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I can now load _basically_ every atom from an entire bacterial cell, into
#blender3d
and
#geometrynodes
via
#molecularnodes
. Each macromolecule is down to atomic detail where available via CellPack, totalling ~250,000,000 points, all rendering (quite quickly) in Cycles
#b3d
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This is actually some really crucial data for my thesis, but like, how am I supposed to present this with a straight face.
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I'm putting dogs as place-holder images while I'm laying out sections of my thesis, and honestly, it really helps with morale.
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Who needs
#alphafold
when you can now just draw your own proteins in
#b3d
using
#geometrynodes
and
#molecularnodes
.
Very excited to have figured this one out. Will be cleaning up and releasing soon hopefully
#blender3d
#sciart
#structuralbiology
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I have managed to create a
#blender3d
plugin for quickly and easily getting structural biology data into
#blender
! It supports models and MD trajectories, and once you have the atoms inside of
#geometrynodes
, you can creative!
Check it out:
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Have you ever wanted to wear GFP as a hat? Well now you can. Playing around in blender and apple’s ARkit on iOS13
#b3d
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Molecular Nodes is stable enough that I've made my first tutorial on how to use it!
Watch the video to see how to get started and import proteins into
#blender3d
and
#geometrynodes
with a single click!
Working towards an animation like this...
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More animation of amino acid side chains based on their B-factors with the Wiggle node. I am so mesmerised by what the result of this node is.
#b3d
#geometrynodes
#sciart
#structuralbiology
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I dropped my falcon tube of sample and now it’s just sitting there like this.... what do I do??
I’ve left it for like an hour because I don’t want to spill more
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Holograms on my poster at
#IUCr2023
If you were unable to chat to me in the first session, will be around again tomorrow.
#MolecularNodes
#GeoemtryNodes
#b3d
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Spent the morning sipping my coffee praying that I had enough RAM to import this monster of a structure into blender. (with success)
Released today
@EMDB_EMPIAR
&
@PDBeurope
, & published
@CellCellPress
, the awesome 3.9 Å
#CryoEM
structure of the
#Flagellar
#Motor
-Hook complex, the molecular machine that drives rotation of the
#Flagellum
for
#Bacterial
motility by Tan et al. from
@ZJU_China
1/2
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Ever wanted to trap a viral capsid inside of a clathrin cage? A new Molecular Nodes tutorial on how to do just that inside of
#blender3d
and
#geometrynodes
.
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several academics have now said to me “but what you’re doing isn’t work” / “you’re a student you’re not working” in relation to my PhD.
Anyone else insulted by this?
Am I wrong in thinking the 50+ hours a week I spend in the lab or on data / reading is work?
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uni: how do we help you graduate?
me: pay phds a living wage and teach relevant skills that aren’t academia only
uni: how about below minimum wage and only paying you for 3 years of a 4 year degree?
me:
uni:
me:
uni: why haven’t you submitted your thesis yet?
#phdchat
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I am so in love with the rendering styles that I can get out of ChimeraX. I can't believe that I stuck with PyMol for so long.
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I can now 'fold' and 'unfold' a crystal structure using
#geometrynodes
and
#molecularnodes
inside of
#b3d
It's just linearly interpolating and there is no checking for steric clashes, but working towards a more 'reaslitic' folding animation
#blender3d
#sciart
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Did you ever want to become part of the electron transport chain? Well now you can! I created this face filter so now you can wear ATP synthase like a hat.
Facebook filter:
Instagram filter:
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Made a DNA generator inside of geometry nodes, but it quickly became complicated and I added in histones, with customisable chromatin that you can just 'draw' in the viewport
#b3d
#geometrynodes
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Updated my render of COVID-19 with some dynamics, virion is now to scale, additional surface proteins and some really nice lipid models thanks to
@JackScienceWalk
. This took 12 hours to render on my computer so hopefully the compression is't too harsh
#b3d
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Refolding proteins with
#blender3d
3.6 beta using using the new
#SimulationNodes
inside of
#GeometryNodes
and
#MolecularNodes
.
Most MD literature ignores the molecular monkey heads that might be present on the nanoscale, but no longer
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Probably my favourite animation I have made to date. Wiggling every single amino acid in an entire virus. Zooming in and out really adds a sense of scale.
Animated and rendered with
#blender3d
#geometrynodes
and
#molecularnodes
.
#SciArt
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Sometimes you have to take time to find time to unwind. Continuing to try and improve the
#geometrynodes
DNA generator. Managed to implement position-dependent unwinding, for helicases, polymerases and the like.
#blender3d
#b3d
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Preparing some videos for upcoming talks. I'll be in Aarhus and Cambridge in the next couple of weeks. Lots of talking about EM data inside of
#blender3d
using
#MolecularNodes
and
#GeometryNodes
to create clear visuals and beautiful animations.
Feels cool to zoom around a cell
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A vanilla
#geometrynodes
physics solver. No vertex weights, no custom scripts or addons, just pure
#b3d
3.2
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Animating histones sliding along procedurally-generated DNA, all inside of
#blender
#b3d
and
#geometrynodes
. Will be releasing some DNA-centric nodes & tutorials very shortly!
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Secondary Structure cartoons are now part of
#MolecularNodes
!
v2.6.0:
Every aspect of these are customisable. Width, thickness, colour, arrows / no arrows, cylinders.
In love with the final result. Done entirely within
#GeometryNodes
and
#Blender3d
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I have now added support for importing full-blown MD topology & trajectory files, from the likes of GROMACS & CHARMM straight into
#blender3d
!
Along with a few other UI & under-the-hood improvements, download v0.5.15 now!
#geometrynodes
#3d
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So I did the final export for my
#IUCr2023
poster and it's... 250 MB.
If you wanna hear what it's all about, come by poster P0049 on Monday or Tuesday next week!
There will be Blender, animated movies, and holograms!
#blender3d
#MolecularNodes
#GeometryNodes
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DNA is now part of Molecular Nodes!
You can extract DNA from structures, procedurally create new DNA, use custom bases, join and break strands, colour it & make it look pretty. All from within
#blender3d
and
#geometrynodes
!
Check it out:
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I keep going on about it, but it just works so ludicrously well. If you have control over the generation of your secondary structure cartoons, you can do sneaky little reveals like this one 🙈🙉
#MolecularNodes
#GeometryNodes
#Blender3d
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I have mountains of emails and messages to respond to from the past few weeks because I've been moving house, but I am just falling more in love with EEVEE instead. Real-time playback of MD simulations with nice lighting & depth of field.
#blender3d
#GeomtryNodes
#MolecularNodes
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Playing around with hallucinating proteins and animating those trajectories inside of
#blender3d
with
#MolecularNodes
#GeometryNodes
Today we're making RF Diffusion, our guided diffusion model for protein design with potential applications in medicine, vaccines & advanced materials, free to use. The software has proven much faster and more capable than prior protein design tools.
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Testing MD rendering styles, focusing on the channel part of an ion channel. Look at those little water molecules go.
Imported with
#molecularnodes
, rendered in
#blender3d
and
#geometrynodes
#b3d
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In 2 hours, I'll be giving my talk for
#BCON22
. You can watch the live stream on the
#blender3d
youtube channel () otherwise the talk should be available shortly after the talk forever.
A sneak peak with
#geometrynodes
and
#molecularnodes
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Is that an alien spaceship, or yet another ridiculously cool protein complex? PDB: 3JC8 type IV pilus complex. Imported and rendered with Molecular Nodes inside of
#blender3d
and
#geometrynodes
#b3d
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CryoEM density inside of
#b3d
and
#MolecularNodes
!
Thanks to code from
@AlisterBurt
and Michael Douglass. Will be coming when Blender 3.5 is released later in March. Potential now also for crystallography electron density as well
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New Blender for Biochemists video is out!
Teaching not only how to make a membrane scene, but to do it procedurally with Geometry Nodes (see live editing in the gif).
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Claymation ATP-synthase rendered through
#molecularnodes
with
#blender3d
and
#geometrynodes
#b3d
#sciart
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Thanks to contributors on the GitHub,
#MolecularNodes
can now import .star files from RELION and cisTEM. You can take your EM images and instance proteins all across the scene, all inside of
#Blender3d
and
#GeometryNodes
Contributed by Johannes Elferich ()
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Help me get to the 2022 Blender Conference in Amsterdam! If you like my Blender tutorials, Molecular Nodes, seeing pretty proteins, and want to see it all on the big stage & to help me get there, donate to my GoFundMe!
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Pushing
#geometrynodes
and
#b3d
to the limit. Utilising instances of instances to animate 200,000,000 atoms procedurally. Animation no longer real-time in viewport, but nothing crashes & can still move around in cycles. New
#molecularnodes
coming soon!
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More testing of CryoEM density inside of
#b3d
via
#MolecularNodes
. Once inside of Blender, it actually works pretty seamlessly with the rest of
#GeometryNodes
. If there are specific 'visualisations' of the EM data you would like to see supported, please let me know :)
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After trying on and off for almost a year, I have FINALLY got secondary structure cartoons for proteins working inside of
#blender3d
and
#GeometryNodes
. Need to test on beta-sheets, then it should make its way to
#MolecularNodes
pretty soon!
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Some of the data that started me on my path to learning
#blender3d
several years ago. I wanted to make beautiful movies of molecular dynamics simulations, to try and show off how cool the science was.
#sciart
#geometrynodes
#b3d
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#molecularnodes
2.0 is released! Completely re-written from the ground up for countless improvements in speed and usability. Can also more easily accept pull requests for those who'd like to contribute.
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Ever wanted to show your EM density maps, as actual densities? Spent the weekend polishing the import of .map files, ready for release in a couple of days with
#blend3d
3.5 release
#MolecularNodes
#GeometryNodes
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Planning out a bunch of
#Blender3d
and
#MolecularNodes
tutorials to get it all up to speed for the updated addon.
What would you like to see covered? Will have a few on the basics, but can expand into particular styles / techniques etc.
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Figured out how to add some jiggle to the AA sidechains, while keeping them _mostly_ 'realistic' and connected.
Still some kinks to work out, but totally procedural 'molecular dynamics' from a static crystal structure. Can scale based on B-factor etc as well
#b3d
#geometrynodes
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I have just released a v0.4 of
#MolecularNodes
, which fixes a fewof bugs and adds a bunch of features! The node tree is auto-generated on import now, making it 1-click and ready to render your protein!:
#blender3d
#geometrynodes
#b3d
#SciArt
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Just released v0.13 of
#molecularnodes
which includes the nodes for casting amino acids to a custom curve. Try your hand at drawing proteins and become the ribosome you always wanted to be:
#b3d
#geometrynodes
#blender3d
#SciArtSeptember
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Adding some side-chain wiggle based on B-factor and proximity. Creates a nice effect for examining a structure. Also they manage to dance along to basically any song you might have playing.
#b3d
#geometrynodes
#sciart
#structuralbiology
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I'm giving a talk in Cambridge next week!
If you are in the area, come along and say hello. I'll be talking about my journey through molecular graphics, with a big focus on the development and use cases of
#MolecularNodes
. Basically an hour of non-stop pretty molecular movies
Don’t miss
@bradyajohnston
’s
#LMBSeminar
, next week on Monday 12th June!
Beginning at 11AM (BST), Brady Johnston will be discussing ‘Building Proteins: Democratising Access to Beautiful Molecular Landscapes.’
More info:
#LMBZoominar
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New version (2.8.0) of
#MolecularNodes
released earlier today. Lots of fixes, with an improvement & overhaul of the biological assemblies and default cartoon styles
#b3d
#GeometryNodes
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A second video showing how to animate multi-state .pdb files and make them disappear in
#blender3d
and
#geometrynodes
with my Molecular Nodes!
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Testing
#molecularnodes
on new structures in
@buildmodels
with and
#geometrynodes
and
#b3d
. PDB: 8EGR rendered in EEVEE in like 30 seconds.
Phage have figured out just the most incredible structures
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May have finally figured out how to get the classic Goodsell style entirely inside of Blender. Still some depth-shading problems to work on though.
#blender3d
#geometrynodes
#molecularnodes
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_finally_ figuring out how to make more stable simulations that work well with other inputs from
#GeomtryNodes
.
Here 'simulating' some histones & DNA being attacked by a carcinogenic monkey head
#b3d
#MolecularNodes
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I have (finally) made a new Blender for Biochemists tutorial. This will be a multi-part series on how to make DNA using geometry nodes.
#b3d
#blender
#geometrynodes
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The wiggle node has been ported over to
#MolecularNodes
2.X, so now you can bring your static crystal structures to life without the need for MD simulations using only
#b3d
and
#geometrynodes
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Have had a lot of fun really diving into the weeds and making an exceedingly complicated procedural membrane generator inside of
#geometrynodes
. Has fake lipid physics that wiggle about, customisable world scale and inputs, and can be applied to any surface
#b3d
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Procedurally generating an infinite crystal structure, based on the unit cell & space group from a .pdb file, all inside of
#blender3d
's
#geometrynodes
. Have been wanting to try and get this working for a while!
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I’m delighted to share our work
@alanbrownhms
on the structures of axoneme, one of the largest macromolecular machine in nature! This is really a dream coming true! Now we have an atomic view of the core of cilia skeleton.
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My next YouTube video on Blender for Biochemists is up!
Exporting models from ChimeraX > Blender, and maintaining atom colours along the way.
Will actually be making more than 1 every year, so comment / tweet @ me with what you would like to see!
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I’ve got a few hours to kill in the airport. Tweet me a PDB id and I’ll make your structure into a face filter for Instagram / Facebook
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Have done some more work on my DNA rig for inside of
#geometrynodes
and
#blender3d
. It now support atomic representations of all 4 of the bases, for ball-and-stick, spherical or surface representations, everything is done 100% procedurally inside of GN.
#sciart
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Some DNA synthesis created & animated entirely in
#blender3d
and
#geometrynodes
with
#molecularnodes
.
Throwing together some very last-minute animations before getting on a plane to
@ComBio2022
. Is anyone else around Melbourne and
#combio
this week?
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My beautiful wiggly jelly bois.
Obviously not accurate interactions, but frankly it's more fun to watch. Love the personality of the arginine on the mid right
#b3d
#GeometryNodes
#SimulationNodes
#MolecularNodes
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One last bug to figure out and fix where some b-sheets change into loops, but I've now fully implemented SS cartoon creation inside of
#GeometryNodes
and
#MolecularNodes
. SS detection needs work. This is currently handled in python. Might need to reimplement in nodes
#blender3d
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The new Wiggle node is now in v0.12 of
#molecularnodes
. I'm super stoked with how this one came out. It adds life to static crystal structures, all based on the underlying B-factors.
#b3d
#geometrynodes
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Had an idea for carboard style DNA / proteins using, which actually turned out super well. Combines
@SouthernShotty
's crafty asset pack with
#molecularnodes
so you get the cool aesthetic with the control of a 3D rig and scientifically accurate data
#b3d
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Combining
#b3d
and
#Eevee
with
#JupyterNotebooks
and
#MolecularNodes
, you can interactively style and render proteins from inside a live notebook.
Actually works a lot better than I thought it might.
#GeometryNodes
inside of python notebooks is a cool combo
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#MolecularNodes
v2.5 is out, which adds support for importing Electron Microscopy densities into
#blender3d
as volumetric objects that work with
#GeometryNodes
. This is 6OGD / EMDB 20053 solved by
@PiperProteins
/
@SarahJ_Piper
MN Release:
1/5
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Visited the
#blender3d
studios post
#BCON22
, ended up standing by the biochemistry poster for an hour giving an impromptu lecture about how amazing proteins are
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#MolecularNodes
is teaming up with the folks at MDAnalysis to offer a potential
#GSOC
project!
If you'd like to potentially get involved with helping create a better integration between Blender and MDAnalysis for visualisation, consider applying to get involved.
MDAnalysis will be in
#GSOC
2024! Do you have experience with
#MD
or other
#simulations
, and like
#coding
to solve problems in
#biophysics
#chemistry
#materials
?
Read our blog on how to apply to work on MDAnalysis:
Pre-proposals are due by March 15th.
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Come on a rollercoaster ride through a viral capsid, to see what those little amino acids are up to.
A sneak peak of what's to come in
#BCON22
talk in a few weeks.
#blender3d
#b3d
#geometrynodes
#molecularnodes
#sciart
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A _very initial_ version of MolecularNodes is now installable via pip.
Checkout the examples linked for how you can do molecular rendering Blender and Molecular Nodes, all within your own jupyter notebooks!
Thanks to
@bradyajohnston
, we can now install
#MolecularNodes
via pip! I just played around with it and made some molecule plots in
@ProjectJupyter
. You can find the notebook on GitHub:
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My second Blender for Biochemists tutorial is now live!
In this we cover some more fundamentals of working in 3D (origin points, vertices / faces, editing a shader) and make the scene on the left! (6LUZ, SARS-cov-2 main protease bound to an inhibitor)
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I’d like to thank everyone for their input, and especially water surface tension for making this a far less messy experience than it needed to be.
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Nothing else is yet implemented, but at least bond lengths and steric clashing are working. Might be able to do some basic, very rough & approximate MD eventually
#GeometryNodes
#MolecularNodes
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Index of Nearest node finally in
#blender3d
simulation nodes branch, means you can finally do some ~~physics~~ inside of
#GeometryNodes
. Testing out some repulsion / attraction and creation of bonds.
Maybe it won't be too long and we can do some rough MD in
#MolecularNodes
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A day off to spend reading
@ChristiansenJen
’s new book on science graphics. Already flicked through and excited to dig through more deeply and take lots of notes
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✅ Compute Hydrogen bond networks
✅ Implement SS detection algorithm
✅ Generate completely customisable cartoon mesh, controllable by the user using fields
A little more testing is needed, but secondary structures are coming to
#MolecularNodes
soon!
#GeometryNodes
#blender3d
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Testing the combination of
#MolecularNodes
and
#blender3d
's new simulation nodes in
#geometrynodes
. Able to get individual amino acids to point wiggle their way to try and get closer to a target, but still obeying their bonds and not breaking anything.
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Had an idea for carboard style DNA / proteins using, which actually turned out super well. Combines
@SouthernShotty
's crafty asset pack with
#molecularnodes
so you get the cool aesthetic with the control of a 3D rig and scientifically accurate data
#b3d
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A few months ago
#b3d
started officially supporting a pip build, which means you can now render using Blender and
#MolecularNodes
via notebooks... very experimental at this stage but lots of potential.
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The first PDB release of 2023 contains only 48 new entries, including this propeller-shaped structure (7utd) of the [NiFe]-hydrogenase Huc from M. smegmatis. View all new entries at
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@dsgoodsell
@buildmodels
Would recommend trying Blender! You can do the whole pipeline in one program
#b3d
#MolecularNodes
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Another Molecular Nodes tutorial on how to import, style and animate the COVID spike protein inside of
#blender3d
and
#geometrynodes
Watch how to install
@mdanalysis
and import molecular dynamics trajectories into Blender, and also make it pretty
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Another Molecular Nodes tutorial, showing how to apply different materials to different parts of your structure to get some cool-looking styles
#blender
#geometrynodes
#b3d
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I'm after any molecular dynamics simulation data for some upcoming talks / videos. Can anyone help me out?
I'm currently after ideally a simulation showing ions passing through an ion channel. Ideally lots of time steps, lots of atoms (waters, ions, EVERYTHING)
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Absolutely wild, but in less than 2 days I have already reached my goal. I'll be going to the Blender conference!!!
I've been contacted by a few groups about doing other talks at institutes while I'm there. Please reach out and I'll see what I can fit in!
Help me get to the 2022 Blender Conference in Amsterdam! If you like my Blender tutorials, Molecular Nodes, seeing pretty proteins, and want to see it all on the big stage & to help me get there, donate to my GoFundMe!
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Made what I like to call a bacterial bad-time generator. Making T4 bacteriophage completely procedurally using
#geometrynodes
#b3d
#blender3d
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Tinkering with DNA inside of
#MolecularNodes
, more molecular monkey heads causing trouble. The new
#GeometryNodes
simulations in
#b3d
open up a lot of potential in terms of molecular animations
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