This is beyond incredible, I hope to get published one day and if so I will do everything I can to use these tools to make that publication look good and get you the attention that you deserve !
Thanks for the kind words mate! I've certainly been thinking about putting a manuscript together at some point that people can reference, but it's pretty low on the list of prioerities. There is a doi through zenodo you can cite though on the github :)
Absolutely crazy addon you've put together, with all the little helpers you put in to control aesthetics and animations. Found out through your talk at blender. It should taught at school!
This is awesome, great to find your channel, I worked at a medical animation studio for many years and enjoying doing it as a hobby and using blender now too. Thanks so much
It's sad to see it stagnate. There hasn't been any visible development on it quite a few years, which was partly the motivation behind me working on this addon (and to get it all working inside of Blender)..
hey Brady, with the new Blender it's hard to get molecular nodes working the way I want. Actually even with V3 I was a bit confused. One big thing I'd like to be able to do but have no idea how is to set different materials for different things: secondary structure, element type, chain. etc. It's thoroughly confusing. Any tips? thanks
I can import the protein but it does NOT create the properties subcategory. Is this cause I use the newest version? Or what is missing? There was also no button for Atomium install in the Addon Menu...
Thank you very much for the great creation of molecular nodes. I folllowed this tutorial until the end but, I could not render the final image of ATP synthase, When I activate the camera I have only the cube!! I appreciate any sugestion. Regards and congratulations for this excellent work
I am new in Blender. I have a question. In 3:59, you have pop up solid, Rendered, Wireframe, Material Preview. Can you tell me how you can I pop up this menu? Thanks in advanced.
How did you switch from 'Solid' to 'Rendered' view at 3:59? Some keyboard shortcut? Also, what would be a good introductory course on Blender that you'd recommend? Thanks
Holding down the 'Z' key and using the menu that pops up. I have a introductory series on my channel targetted at people coming from biology, you can start here: ua-cam.com/video/CfkjBoOaw0g/v-deo.html
Just trying this out for the first time in Blender 3.4.1 with MN v2.3.0. When following this video and the documentation the node groups don't exactly match. For example I don't see the MOL_prop_setup node group in the tree, or as an available node in the list. What am I missing?
The addon has been updated and no longer requires those nodes, which simplifies everything a bit. I haven’t had the time to update the tutorials though! The workflow is mostly the same but some of the nodes and interface has changed around a bit
Might be that the element definititions are strange in the file that you are opening. If you can open a issue on the github page I can help you better there!
Impressive! However, it's really fast and difficult to follow especially when I am not familiar with the blender. It would be nice for newbies if you could also mention what you were doing i.e. shift+right click. At the 4:00, I don't even know how to get those icon to select up and really have no idea the keyword to search on google. I only hope that in the future if you're going to make another version for newbies would be really nice. Thanks
Thanks for the feedback! This is something I have been thinking about. I kind of need a series that starts with Molecular Nodes for someone who isn't familiar with Blender, but also a series that starts with Molecular Nodes for someone who is familiar with Blender. It's on the list of things to do, but it also doubles the workload. Here is a great place to start with Blender in General: ua-cam.com/video/CfkjBoOaw0g/v-deo.html I've got a whole series for starting out with Blender in general if you want to look through the channel. They are all a little outdated unfortunately. Currently in thesis-writing mode so I won't be able to get anything out for the next couple of months most likely.
@@BradyJohnston I wish you all the best in writing your thesis and thank you for all the greatness you have contributed to this field. Really appreciate it.
If you are on an M1 or M2 MacBook, then there are problems with installation. Check the installation instructions on how to fix this: bradyajohnston.github.io/MolecularNodes/installation.html#installing-biotite-mdanalysis and if the issue persists please check & report the issue via the GitHub page
I just found out about this amazing addon, bruh, you've already improved it so much!! Thank you, not only for making the addon, but also for these tutorials! Keep up the good work.
Thank you for the great tool and tutorials! As I understood, it is not possible to view the structure as helices and sheets (arrows) in molecular nodes, right?
There is the ribbon / licorice representation, but in order to show the arrows / alpha helices etc I need to try and detect the secondary structure which is actually quite a complex task unfortunately. Hopefully a feature that will come in future releases if I can figure it out!
It is in the files you download from the PDB, but for molecular dynamics & other kinds of animations the secondary structure needs to be calculated for each frame which is difficult. I may end only dealing with the encoded information from the PDB. Still a work in progress!
@@BradyJohnston I see thank you! I actually did not think about the dynamics, I just thought of having a steady structure as I would export from Chimera or somewhere else.
Dear Brady, I am really interested in your videos, I was trying to install MolecularNodes in Blender using Ubuntu. However, still I couldn't install it?
Hi Brady, while attempting this tutorial, I couldn't find the "chain_number" in the properties node to connect it with the "ID" of the Random value node. Rather, there's a "Named attribute" node which is connected with the "ID" of the random node. Also, how to render molecular nodes in the EEVEE mode?
Such a great addon. This simplifies greatly my workflow to get complex molecules into blender! As a non-native english speaker, I can understand all of your tutorials, you speak so clearly,
thanks mate! The surface isn't done by any of the 'traditional' methods from other molecular graphics software. This converts all of the atoms to a point-density field based on their atomic radius, and then generates a mesh which encloses that density. Would be most similar to the space-filling surface representation I believe. I haven't figured out how I could do other surfaces yet.
It depends on the style you are after. There is an `Atoms EEVEE` node for showing the atoms in EEVEE, otherwise the other styles should all work in EEVEE as well except the `Atoms Cycles`. As for particular rendering settings, I suggest looking at other EEVEE-specific tutorials on youtube to get the look you are after
Great add-one. Thanks a lot. One question: maybe I missed it but is there a way to select and change the ligand? I can see my ligand is imported with the protein file but it's part of the protein mesh
You can manually separate the ligand my selecting the mesh which is the ligand, or you can do it entirely within Geometry Nodes. There will be a "Ligands" node under Selections. See more here (ua-cam.com/video/ruzrQ6uKvDQ/v-deo.html&)
This is beyond incredible, I hope to get published one day and if so I will do everything I can to use these tools to make that publication look good and get you the attention that you deserve !
Thanks for the kind words mate! I've certainly been thinking about putting a manuscript together at some point that people can reference, but it's pretty low on the list of prioerities. There is a doi through zenodo you can cite though on the github :)
Absolutely crazy addon you've put together, with all the little helpers you put in to control aesthetics and animations. Found out through your talk at blender. It should taught at school!
thanks so much mate! hopefully you can put it to good use :)
@@BradyJohnston Already have!
Awesome work Brady… Keep it up👏🏼😎🙌🏼
Thanks! Will do!
Keep up the great work! Excellent tutorials. Seeing the new vid drop made my day🤘
This is awesome, great to find your channel, I worked at a medical animation studio for many years and enjoying doing it as a hobby and using blender now too. Thanks so much
Hopefully it helps you keep making cool stuff!
This video is awesome you are seriously talented, very grateful to have a resource like this. Also nice CGMatter shoutout I love that guy
This is powerful! Great job
Thank you so much!
Awesome. Still learning the basics of Blender. Brilliant use of geometry nodes. Maybe this is why Molecular Maya hasn't been brought forward.
It's sad to see it stagnate. There hasn't been any visible development on it quite a few years, which was partly the motivation behind me working on this addon (and to get it all working inside of Blender)..
That is really cool! Excellent work.
hey Brady, with the new Blender it's hard to get molecular nodes working the way I want. Actually even with V3 I was a bit confused. One big thing I'd like to be able to do but have no idea how is to set different materials for different things: secondary structure, element type, chain. etc. It's thoroughly confusing. Any tips? thanks
Best channel of biological Blender tutorials ever. Can't wait to see it grow bigger💪
Appreciate that! Hopefully lots more to come :)
You need more subs this is great work.
I can import the protein but it does NOT create the properties subcategory. Is this cause I use the newest version? Or what is missing? There was also no button for Atomium install in the Addon Menu...
Thank you very much for the great creation of molecular nodes. I folllowed this tutorial until the end but, I could not render the final image of ATP synthase, When I activate the camera I have only the cube!! I appreciate any sugestion. Regards and congratulations for this excellent work
THANK YOU!! Phenomenal work.
Thanks so much! Glad it is useful!
Fantastic! Thanks so much for creating (:
I am new in Blender. I have a question. In 3:59, you have pop up solid, Rendered, Wireframe, Material Preview. Can you tell me how you can I pop up this menu? Thanks in advanced.
hi Brady! when importing cryo-EM density is it possible to later convert it to a mesh so that I can apply modifiers, edit the mesh, etc?
How did you switch from 'Solid' to 'Rendered' view at 3:59? Some keyboard shortcut? Also, what would be a good introductory course on Blender that you'd recommend? Thanks
Holding down the 'Z' key and using the menu that pops up. I have a introductory series on my channel targetted at people coming from biology, you can start here: ua-cam.com/video/CfkjBoOaw0g/v-deo.html
@@BradyJohnston Thanks! This tutorial was pretty useful. Godspeed on your future videos / projects good man.
Another question. Is it possible to colour a protein of one chain in ribbon style?
hard to follow in blender 4.2....
Just trying this out for the first time in Blender 3.4.1 with MN v2.3.0. When following this video and the documentation the node groups don't exactly match. For example I don't see the MOL_prop_setup node group in the tree, or as an available node in the list. What am I missing?
The addon has been updated and no longer requires those nodes, which simplifies everything a bit. I haven’t had the time to update the tutorials though! The workflow is mostly the same but some of the nodes and interface has changed around a bit
Love your work! One question when I import a protein my turns out black and not coloured in cycles. Any idea why that could be happening?
Might be that the element definititions are strange in the file that you are opening. If you can open a issue on the github page I can help you better there!
Impressive! However, it's really fast and difficult to follow especially when I am not familiar with the blender. It would be nice for newbies if you could also mention what you were doing i.e.
shift+right click. At the 4:00, I don't even know how to get those icon to select up and really have no idea the keyword to search on google. I only hope that in the future if you're going to make another version for newbies would be really nice. Thanks
Thanks for the feedback! This is something I have been thinking about. I kind of need a series that starts with Molecular Nodes for someone who isn't familiar with Blender, but also a series that starts with Molecular Nodes for someone who is familiar with Blender. It's on the list of things to do, but it also doubles the workload. Here is a great place to start with Blender in General: ua-cam.com/video/CfkjBoOaw0g/v-deo.html
I've got a whole series for starting out with Blender in general if you want to look through the channel. They are all a little outdated unfortunately. Currently in thesis-writing mode so I won't be able to get anything out for the next couple of months most likely.
@@BradyJohnston I wish you all the best in writing your thesis and thank you for all the greatness you have contributed to this field. Really appreciate it.
What shortcut you use to create "join geometry" node at 12:31?
Node wrangler! Learn all about it here: ua-cam.com/video/3zz2b9NFqB0/v-deo.html
Didn't work for me on a Macbook to install the packages :(
If you are on an M1 or M2 MacBook, then there are problems with installation. Check the installation instructions on how to fix this: bradyajohnston.github.io/MolecularNodes/installation.html#installing-biotite-mdanalysis and if the issue persists please check & report the issue via the GitHub page
My hero
Please make a tutorial with MN2.0
working on it! lots of things to do and not a lot of time to do them
Yus!
Looking forward to seeing the more detailed videos on smaller topics of Molecular Blender❤️❤️❤️
Coming soon! Lots in the works :)
I just found out about this amazing addon, bruh, you've already improved it so much!! Thank you, not only for making the addon, but also for these tutorials! Keep up the good work.
amazing , thank you brady !
Thank you for the great tool and tutorials! As I understood, it is not possible to view the structure as helices and sheets (arrows) in molecular nodes, right?
There is the ribbon / licorice representation, but in order to show the arrows / alpha helices etc I need to try and detect the secondary structure which is actually quite a complex task unfortunately. Hopefully a feature that will come in future releases if I can figure it out!
Thank you! I always thought that this information would be encoded in the PDB format.
It is in the files you download from the PDB, but for molecular dynamics & other kinds of animations the secondary structure needs to be calculated for each frame which is difficult. I may end only dealing with the encoded information from the PDB. Still a work in progress!
@@BradyJohnston I see thank you! I actually did not think about the dynamics, I just thought of having a steady structure as I would export from Chimera or somewhere else.
Dear Brady, I am really interested in your videos, I was trying to install MolecularNodes in Blender using Ubuntu. However, still I couldn't install it?
Hi Brady, while attempting this tutorial, I couldn't find the "chain_number" in the properties node to connect it with the "ID" of the Random value node.
Rather, there's a "Named attribute" node which is connected with the "ID" of the random node.
Also, how to render molecular nodes in the EEVEE mode?
So bloody cool. If only that technology existed during my time..oh well, never too late. Amazing work ❤
woah - this is amazing. thanks so much for creating this, you absolute superstar! :)
it would be also kool if you used UE4 for make a "simulation" of cell mitosis
Such a great addon. This simplifies greatly my workflow to get complex molecules into blender! As a non-native english speaker, I can understand all of your tutorials, you speak so clearly,
Glad it helped! And I'm glad the tutorials are clear to follow :)
Amazing man
Great work! Thank you Brady. Just a quick question: how is the surface calculated?
thanks mate! The surface isn't done by any of the 'traditional' methods from other molecular graphics software. This converts all of the atoms to a point-density field based on their atomic radius, and then generates a mesh which encloses that density. Would be most similar to the space-filling surface representation I believe. I haven't figured out how I could do other surfaces yet.
Incredible work! How can we view and render this in Eevee?
It depends on the style you are after. There is an `Atoms EEVEE` node for showing the atoms in EEVEE, otherwise the other styles should all work in EEVEE as well except the `Atoms Cycles`. As for particular rendering settings, I suggest looking at other EEVEE-specific tutorials on youtube to get the look you are after
Great add-one. Thanks a lot. One question: maybe I missed it but is there a way to select and change the ligand? I can see my ligand is imported with the protein file but it's part of the protein mesh
You can manually separate the ligand my selecting the mesh which is the ligand, or you can do it entirely within Geometry Nodes. There will be a "Ligands" node under Selections. See more here (ua-cam.com/video/ruzrQ6uKvDQ/v-deo.html&)
@@BradyJohnston Thank you very much Brady. Great work.
Insane job this looks amazing
Thanks mate!
Great work and add-on! Congrats
Thank you!