For anyone working on newer versions of blender (3.0+), the "Point Instance" node has been replaced (used at ~11:50). If you set up "Object Info" to input the lipid, and pipe it into "Geometry to Instance" and then "Instance on Points", you can re-create what Brady is doing.
@Miguel Rosado It's confusing, but you need to plug both ("Distribute Points on face" and "Object Info" > "Instances of Points" > "join Geometry". General rule of thumb, when connecting nodes the input's and output's colors (small colored shapes on the sides on the nodes) should match.
Comments are where it is AT!!! Thank you. If it helps anyone the path is: "Distribute points on faces" (green point to point) >instance on points (with Object info off to the side, green "geometry" plug into Instance on points "instance" plug)> join geometry.
Truth be told, I commented before I got to that part and gave up on the second layer! The latest blender update has changed so much, I couldn't piece it together. I just used the top layer for a cell surface and it was good enough for my purposes. One other tip, don't bother with Bioblender add on if you see it (it's another membrane tutorial/product). It doesn't actually work with the latest version of Blender. If you do end up figuring it out, comment back! @@Bsmalls4142
@@BradyJohnston I am a total beginner with blender but thanks to your tutorials I started playing around a bit. I know that to import EM maps into Cinema4D from Chimera one could save them as scene and export them as .WRL. I wonder if that is as smooth in blender as well.
You deserve much more subscribers. Great work. I am a doctor and I use Blender to teach intricate medical concepts to my students. Your videos are incredibly helpful for me.
You've inspired me! I have my MSc thesis defence coming up in a few weeks, and I think I'm going to try and apply this to illustrate some extracellular vesicle things. Please, keep 'em coming!
@@BradyJohnston I couldn't figure out how to randomly rotate my phospholipids around the normals when using the "Align Rotation to Vector" node (the only way I found to have them all oriented in a concentric way around my isosphere). These geometry nodes are incredibly powerful, but there are things I can't seem to be able to do. I'm not sure if it's because it's impossible or because I don't know enough "usage patterns". Your videos are extremely helpful and make it so much easier to apply my learnings-- it seems silly, but just doing examples of biochem applications is a thousand times more helpful than tutorials on how to make a donut or a car. Thanks again, and please keep these videos going! 🙏🏻
Really nice tutorial. Have you found a good way to instance the protein and prevent instancing of the phospholipid at those points? I tried Mesh Boolean with Realize Instances in geonodes which works but its not performant.
Brady, I work with Blender and lately i've been doing lots of work related to microbiology, due to the Covid. It'd be really nice to see more videos explaining how to use Blender in this field, specially because I'm always afraid of committing any incoherence when developing the models. More information about how to represent viruses and other microorganisms would help to spread correct information. Thanks!
Hi brady. Is there a way to project the lipids along the normals of the plane? Because if I curve the membrane too much it becomes visible that the lipids are all oriented vertically in respect to the world but do not follow the bend of the plane
Thank you for your tutorial! However, after blender 3.0, many functions of the point geometry node have disappeared, so could you give another solution? thanks
Thanks for the kind words! I certainly would. I haven't done any cryoEM myself so I haven't dealt with their maps much - but I would certainly happily play around with them inside of blender.
Brady, how can I cut a the membrane-bound protein such that the cross-section view is revealed? I have been trying to use boolean-subtract with no success. Whenever I apply it, the whole protein disappears.
Whenever I import the protein from the chimera file my protein is colur and not colourless like you showed in your tutorial, I am having a hard time changing its colour in the shader editor can anyone help me with this.
I just discovered your work, but I really like what I'm seeing. I think so many researchers underestimate the importance of having good illustrations. It's also important in the context of science communication, and in making science look more appealing to a wider audience. Also, I'm a (soon to be) medicinal chemist, so seeing the tweet about MDanalysis support for importing trajectories and stuff into Blender really piqued my interest. Would love to see a video on how to do that
Hi. Geometry nodes are not the same in the 3.3.1. Point distribution and Point instance are not exactly the same and the results are wrong desíte I tried all the options. Any suggestion? Thanks
Thank you for showing how to make it procedural, makes things a lot easier when adjusting the scene. What are the extra options now that 2.93 is out? What I have seen so far is as great as your video is showing. Would love to know more!
Great tutorial. I really appreciate your hard work for doing this. I have a question, once we import a protein structure from protein data bank or our own PDB file, Blender converts it in a surface view form. Is it possible to maintain some portion of a transmembrane protein in cartoon view and some in surface view while we insert the protein in bilayer? Thanks!
You will have to do two separate exports from chimeraX. One with the portion of the protein as a cartoon, and then one with the portion of the protein as a surface. You could also try out the new addon that I've been working on that lets you change representation after import into Blender: ruclips.net/video/ruzrQ6uKvDQ/видео.html
hi Brandy You super techer. I have Problem witch new Blender 3.1 and make Poit Object. How i can do it in new Blender 3.1 ? Point instance its no ther. Than you for you Answer A
Great job brother! I really appreciate your effort here and I hope that you focus on more lipid dynamics in future Blender for Biochemists videos. It would be awesome if you could generate a bisected chloroplast with the inner and outer envelope membranes! Maybe you could even fit a thylakoid membrane as well?
That's the plan! I have been working on some new membrane-specific nodes recently, so will be releasing them & doing some tutorials in the coming weeks :)
Very interesting, but I'm greedy. I've made membranes similar to this, (albeit not procedurally) and key framed the wave modifier to give a nice undulation to the membrane. What I'd really like though is to be able to have the lipid and protein molecules randomly moving about in X and Y direction and bouncing off each other as rigid bodies, so they never overlapped. Is there an easy way to achieve that via geometry nodes?
Sadly not through geometry nodes as there is no physics simulation support in geometry nodes (not yet). You can look into it with particle systems and the like, but it will also be a lot of work for a small amount of gain. I've done some stuff before with particle systems / molecular scripts, but you can't simulate a very big membrane scene because it very quickly becomes a molecular dynamics simulation that takes a super-computer to run.
There is a hackey-way at the moment using vector math and scaling them to 0. There is a far better way to do it coming in 2.93 update so I thought I might leave it until then.
Great work Brady! You are an excellent teacher. Was very easy to follow. I did however run into a problem when I tried to take it a step further. I tried animating the lipid bilayer by having a rotating empty drive the displacement. Then the protein molecules started flipping/spinning uncontrollably, i.e. they are not locked into place on the membrane. Do you have a suggestion how to get around this? Cheers,
Thanks for the kind comment! In the current method of doing it, geometry nodes as a modifier is being applied _after_ the displacement modifier. This means that every time the displacement modifier is being changed (animating the texture) then geometry nodes re-generates the scene (causing things to move erratically all over the place). I haven't found a way to effectively animate the membrane in Blender 2.93. However! In the next release, they are including nodes inside geometry nodes that can take textures as an input. Meaning we can create the membrane, _then_ displace it all inside geometry nodes. This solves the problem - but I thought I would leave that out of the video until it comes in the next release :)
No worries, Brady! Great news about the upcoming new nodes. Hope the next release comes soon! It is really exciting times, seeing how rapidly Blender is evolving. Cheers from Mats at Magipics
Love it, this is by far one of the best channels on RUclips. Would you do a small animation of the coronavirus cell getting destroyed?? I've been longing to see this, I hope this also happens in reality...
Hey Brady great tutorial! I am ran into an issue though. To the membrane plane i applied a curve modifier, so that the plane has an S shape. My problem is that the instanced lipids do no stay perpendicular/tangent to the plane but stay parallel to Z, and thus do not follow the shape i gave to plane. Do you have a solution for that? Thanks in advance!
Hello! Yes this is a problem at the moment. With this set up we are displacing the lipids only on the Z axis, so once you start working with not just a flat plane things don't work any more. I forgot to mention this in the video - but mostly it is currently limited to a flat plane. You can do some hacky-fixes for it to get it ~kind~ of working, but not great at the moment using Normals. The updates to Geometry Nodes in blender 2.93 (coming in a few months) will make this much more usable and easier to do. I'll do an update video when that comes out :)
@Termite68 There is a similar approach from GC figures. He made it work with a threedimensional shape using the addon: GScatter. ruclips.net/video/G_Ue5e9cR0o/видео.html It is actually a relativly new Video. 5 months ago it probably hasnt exist yet.
My PhD was all mitochondrial genomics so this is a godsend. Wish I had a computer capable of actually doing fun stuff in blender for job talk presentations. Saw an example on reddit and was like damn that's so much better than my 2D adobe animate videos. The iMac that I got from lab when my PI retired 1000% can't handle this, but it generally accepted everything until I got to the point where it wanted to distribute the ATPase subunit I imported. Decided I'd just stick with one haha.
Yes it can get computationally pretty intensive pretty quickly. There are some tricks to making things run smoothly that I should hopefully be covering in future videos!
For anyone working on newer versions of blender (3.0+), the "Point Instance" node has been replaced (used at ~11:50). If you set up "Object Info" to input the lipid, and pipe it into "Geometry to Instance" and then "Instance on Points", you can re-create what Brady is doing.
@Miguel Rosado It's confusing, but you need to plug both ("Distribute Points on face" and "Object Info" > "Instances of Points" > "join Geometry". General rule of thumb, when connecting nodes the input's and output's colors (small colored shapes on the sides on the nodes) should match.
Life saver! Thankss
Comments are where it is AT!!! Thank you. If it helps anyone the path is: "Distribute points on faces" (green point to point) >instance on points (with Object info off to the side, green "geometry" plug into Instance on points "instance" plug)> join geometry.
but how to duplicate and have the second layer on the bottom... having some trouble there.@@hollypbird
Truth be told, I commented before I got to that part and gave up on the second layer! The latest blender update has changed so much, I couldn't piece it together. I just used the top layer for a cell surface and it was good enough for my purposes. One other tip, don't bother with Bioblender add on if you see it (it's another membrane tutorial/product). It doesn't actually work with the latest version of Blender. If you do end up figuring it out, comment back! @@Bsmalls4142
Oh you know I'm here for the geometry nodes.
I really had to resist doing a video using the 2.93alpha, geomtry nodes is just the greatest. Will just have to update it when it all comes out.
@@BradyJohnston I am a total beginner with blender but thanks to your tutorials I started playing around a bit. I know that to import EM maps into Cinema4D from Chimera one could save them as scene and export them as .WRL. I wonder if that is as smooth in blender as well.
You deserve much more subscribers. Great work. I am a doctor and I use Blender to teach intricate medical concepts to my students. Your videos are incredibly helpful for me.
This is amazing! Would love to see how you'd zoom in and highlight phosphorylation of intracellular residues of these receptors.
Great work Brady keep it up we love To see more
Thanks! I will make sure there is more to come :)
Very cool, love seeing this specific demonstration of the Join node, as most people I've seen don't use it much besides getting original mesh back.
great, can't wait to get started on membranes. Thanks for the tutorial.
You've inspired me! I have my MSc thesis defence coming up in a few weeks, and I think I'm going to try and apply this to illustrate some extracellular vesicle things. Please, keep 'em coming!
Good luck! Please do share what you come up with :)
@@BradyJohnston Here's the first presentable image I made: en.wikipedia.org/wiki/File:Exosome_with_hsp70.png
Looks fantastic! Nice work :)
@@BradyJohnston I couldn't figure out how to randomly rotate my phospholipids around the normals when using the "Align Rotation to Vector" node (the only way I found to have them all oriented in a concentric way around my isosphere). These geometry nodes are incredibly powerful, but there are things I can't seem to be able to do. I'm not sure if it's because it's impossible or because I don't know enough "usage patterns". Your videos are extremely helpful and make it so much easier to apply my learnings-- it seems silly, but just doing examples of biochem applications is a thousand times more helpful than tutorials on how to make a donut or a car. Thanks again, and please keep these videos going! 🙏🏻
Great tutorial! Also, all the little side tips and tricks you mention are very helpful.
Awesome tutorial 🤙 Would love to see you build on that project to make a more complex membrane
Will make sure to follow it up soon :)
+1 and also +1 for animation of the molecules and/or panning a new zooming the camera to make video clips. Amazing work!
i fell in love with blender. We need to start learining this at university. This is awsome.
Stunning! Really brilliant work. Thank you so much for walking us through this!
Insane in the Membrane
Really nice tutorial. Have you found a good way to instance the protein and prevent instancing of the phospholipid at those points? I tried Mesh Boolean with Realize Instances in geonodes which works but its not performant.
awesome to see how you applied geometry nodes for your work! well done!
Thanks!
Brady, I work with Blender and lately i've been doing lots of work related to microbiology, due to the Covid. It'd be really nice to see more videos explaining how to use Blender in this field, specially because I'm always afraid of committing any incoherence when developing the models. More information about how to represent viruses and other microorganisms would help to spread correct information. Thanks!
This series is so amazing please keep uploading!
Thanks so much! I will make sure that I do :)
This is brilliant! Looking forward to the MD animation.
As a fanatic of fancy shading, i'd love to have seen some subsurface scattering on that
I might dive into more fancy shading / setting up a nicer seen later on. VIdeo was already long and wanted to keep things relatively straight forward
Hi brady. Is there a way to project the lipids along the normals of the plane? Because if I curve the membrane too much it becomes visible that the lipids are all oriented vertically in respect to the world but do not follow the bend of the plane
great stuff but where r the new videos???
Thank you for your tutorial! However, after blender 3.0, many functions of the point geometry node have disappeared, so could you give another solution? thanks
Came across the same difficulty but found an explanation here: ruclips.net/video/Yci5ouEmnLI/видео.html
@@justusme thanks a lot!
I haven't done so yet, but will hopefully be remaking this tutorial sometime soon with the new fields :)
Wow this is genuinely amazing, I need to get stuck in to blender. Thank you for making such informative videos!! Looking forward to more content
Absolutely stunning, thanks for sharing! Would you consider making a video on how to deal with cryoEM volume maps?
Thanks for the kind words! I certainly would. I haven't done any cryoEM myself so I haven't dealt with their maps much - but I would certainly happily play around with them inside of blender.
Thank you so much for this video, it is exactly what I need to generate the a visualization for my research.
Glad it was helpful!
These videos are amazing. I wish you could produce more content, especially also into making animations/scenes!
Brady, how can I cut a the membrane-bound protein such that the cross-section view is revealed?
I have been trying to use boolean-subtract with no success. Whenever I apply it, the whole protein disappears.
maybe try using the knife bisect tool?
Whenever I import the protein from the chimera file my protein is colur and not colourless like you showed in your tutorial, I am having a hard time changing its colour in the shader editor can anyone help me with this.
Hey brady, great tutorial ty!
I just discovered your work, but I really like what I'm seeing. I think so many researchers underestimate the importance of having good illustrations. It's also important in the context of science communication, and in making science look more appealing to a wider audience. Also, I'm a (soon to be) medicinal chemist, so seeing the tweet about MDanalysis support for importing trajectories and stuff into Blender really piqued my interest. Would love to see a video on how to do that
late to reply, but there is now a video on exactly how to do that if you haven't seen it :) ruclips.net/video/O7DpooCF2OI/видео.html
Hi. Geometry nodes are not the same in the 3.3.1. Point distribution and Point instance are not exactly the same and the results are wrong desíte I tried all the options. Any suggestion? Thanks
Thank you for showing how to make it procedural, makes things a lot easier when adjusting the scene. What are the extra options now that 2.93 is out? What I have seen so far is as great as your video is showing. Would love to know more!
Thanks! It was so helpful in my project~! I wish I can see more tutorials~
Great tutorial! Very cool. Also thanks for putting up the whole +40 mins progress 💯
Thanks mate! Glad people appreciate the longer videos I was feeling bad it was so long
They removed the “Point Instance” option so I’m stuck! Anyone know how to solve this in the latest version?
Mind blowing! Thanks for the tutorial!
Thanks mate! Glad it is useful :)
Great tutorial. I really appreciate your hard work for doing this. I have a question, once we import a protein structure from protein data bank or our own PDB file, Blender converts it in a surface view form. Is it possible to maintain some portion of a transmembrane protein in cartoon view and some in surface view while we insert the protein in bilayer?
Thanks!
You will have to do two separate exports from chimeraX. One with the portion of the protein as a cartoon, and then one with the portion of the protein as a surface. You could also try out the new addon that I've been working on that lets you change representation after import into Blender: ruclips.net/video/ruzrQ6uKvDQ/видео.html
Looks amazing
Thanks! Hope it is useful :)
YEEESS
I had to do this same two years ago, but used hair particles and two separate layers (which is kinda slow)
This could saved me a lot of time
great video
hi Brandy
You super techer. I have Problem witch new Blender 3.1 and make Poit Object.
How i can do it in new Blender 3.1 ? Point instance its no ther.
Than you for you Answer
A
Great job brother! I really appreciate your effort here and I hope that you focus on more lipid dynamics in future Blender for Biochemists videos.
It would be awesome if you could generate a bisected chloroplast with the inner and outer envelope membranes! Maybe you could even fit a thylakoid membrane as well?
That's the plan! I have been working on some new membrane-specific nodes recently, so will be releasing them & doing some tutorials in the coming weeks :)
Very clear and effective, looking forward to playing with it myself! Keep up the great content :D
Thank you so much!
Wow! This looks amazing. Thanks for making this tutorial
Thanks!
amazing. thanks
Thank you so much for the great tutorial!
You are welcome! More great tutorials to come :)
Very interesting, but I'm greedy. I've made membranes similar to this, (albeit not procedurally) and key framed the wave modifier to give a nice undulation to the membrane. What I'd really like though is to be able to have the lipid and protein molecules randomly moving about in X and Y direction and bouncing off each other as rigid bodies, so they never overlapped. Is there an easy way to achieve that via geometry nodes?
Sadly not through geometry nodes as there is no physics simulation support in geometry nodes (not yet).
You can look into it with particle systems and the like, but it will also be a lot of work for a small amount of gain. I've done some stuff before with particle systems / molecular scripts, but you can't simulate a very big membrane scene because it very quickly becomes a molecular dynamics simulation that takes a super-computer to run.
@@BradyJohnston OK Thanks. I'll just have to be patient.
@@jimcoote5094 Yep things are moving and developing fast, but some times not fast enough!
Is there any simple way of avoiding overlap between, for example, the proteins and the lipids?
There is a hackey-way at the moment using vector math and scaling them to 0. There is a far better way to do it coming in 2.93 update so I thought I might leave it until then.
Amazing! Thanks a lot
This is really great
Great work Brady! You are an excellent teacher. Was very easy to follow.
I did however run into a problem when I tried to take it a step further. I tried animating the lipid bilayer by having a rotating empty drive the displacement. Then the protein molecules started flipping/spinning uncontrollably, i.e. they are not locked into place on the membrane. Do you have a suggestion how to get around this?
Cheers,
Thanks for the kind comment!
In the current method of doing it, geometry nodes as a modifier is being applied _after_ the displacement modifier. This means that every time the displacement modifier is being changed (animating the texture) then geometry nodes re-generates the scene (causing things to move erratically all over the place). I haven't found a way to effectively animate the membrane in Blender 2.93.
However! In the next release, they are including nodes inside geometry nodes that can take textures as an input. Meaning we can create the membrane, _then_ displace it all inside geometry nodes. This solves the problem - but I thought I would leave that out of the video until it comes in the next release :)
No worries, Brady!
Great news about the upcoming new nodes. Hope the next release comes soon!
It is really exciting times, seeing how rapidly Blender is evolving.
Cheers from Mats at Magipics
Love it, this is by far one of the best channels on RUclips. Would you do a small animation of the coronavirus cell getting destroyed?? I've been longing to see this, I hope this also happens in reality...
I want to slowly work up to such an animation, so some time in the future!
Mind-Blown. Big THANK YOU! #3d #blender
Glad it helped!
Hey Brady great tutorial! I am ran into an issue though.
To the membrane plane i applied a curve modifier, so that the plane has an S shape. My problem is that the instanced lipids do no stay perpendicular/tangent to the plane but stay parallel to Z, and thus do not follow the shape i gave to plane.
Do you have a solution for that?
Thanks in advance!
Hello! Yes this is a problem at the moment. With this set up we are displacing the lipids only on the Z axis, so once you start working with not just a flat plane things don't work any more.
I forgot to mention this in the video - but mostly it is currently limited to a flat plane. You can do some hacky-fixes for it to get it ~kind~ of working, but not great at the moment using Normals. The updates to Geometry Nodes in blender 2.93 (coming in a few months) will make this much more usable and easier to do. I'll do an update video when that comes out :)
@@BradyJohnston ok great ! Thank you for the answer !
@Termite68 There is a similar approach from GC figures. He made it work with a threedimensional shape using the addon: GScatter. ruclips.net/video/G_Ue5e9cR0o/видео.html
It is actually a relativly new Video. 5 months ago it probably hasnt exist yet.
@@lukasfesenmeier301 Thanks ! I will definitely have a look !
dude this is amazing, i will be studying this
Thanks mate! I hope it is helpful. More videos to come :)
20:48 dog barking in the background?? 😍
great tutorial- thank you for making this
There are a few dogs around on my street :P glad you liked the video!
My PhD was all mitochondrial genomics so this is a godsend. Wish I had a computer capable of actually doing fun stuff in blender for job talk presentations. Saw an example on reddit and was like damn that's so much better than my 2D adobe animate videos. The iMac that I got from lab when my PI retired 1000% can't handle this, but it generally accepted everything until I got to the point where it wanted to distribute the ATPase subunit I imported. Decided I'd just stick with one haha.
Yes it can get computationally pretty intensive pretty quickly. There are some tricks to making things run smoothly that I should hopefully be covering in future videos!
This was super cool! My colleagues are gonna wet themselves when they see this! Thanks!
I'm glad! Pease do share what you managed ot make :)
@@BradyJohnston Sure, are you on IG? Im using IG to post blender stuff.
@@sampomuranen1 @bunchofbradys on ig
Thanks a lot man
Happy to help
Do you have a patreon or something similar
I didn't - but I do now! If you'd like to support me: www.buymeacoffee.com/bradyajohnston
Great!
This is insane.
11:06 "pu-us-on" - but with a French accent. Nice video!
Will practice my pronunciation for the next video!
than you so much! very powerfull! im dreaming last night in geometry nodes world.
Thanks! I too dream in geometry nodes - it's a fascinating world :)
Wicked !!
Came here from clockwork!
For me it is a pie. lololol Great tut!!!
Please subtitle indonesia :'(
Apologies but I am currently relying upon the auto-generated captions from RUclips, I am unsure if Indonesian is available for that or not.
you are so smart and handsome