Molecular Nodes | Animation Proteins | Blender for Biochemists | Geometry Nodes

[@R-Tex.]

The amount of thought, knowledge, and experimentation that must've gone into creating this add-on is mind-boggling. Once again, thank you for the add-on and these comprehensive & detailed tutorials.

[@entr0pic]

Two videos in one day?? Amazing

[@BradyJohnston]

The man can't be stopped

[@BradyJohnston]

it turns out it's way quicker to make and edit a video when you limit yourself to only recording for like 15 minutes

[@entr0pic]

@@BradyJohnston I love that for you, keep up the good work but take rests when u need to ⭐️

[@worldkeyvideo9080]

amazing work I just tried out the same process using a hemoglobin protein and it worked great! I am very impressed. this is an amazing tool!

[@BradyJohnston]

Thanks for the kind words! I'm glad that it's working well, and please share any fabulous results that you manage to make!

[@lastmohican4679]

Excellent job, and thank you very much. I'm curious if it's possible to rig and animate proteins?

[@SamSpaeth]

Incredible work, and greatly user friendly. thank you. coffee coming right up, milk and sugar?

[@BradyJohnston]

Oat milk, no sugar, extra short :)

[@lifesciencegraphics]

Hi and thank you very much for this tutorial and the awesome addon. I started with 0.10.4 and noticed that the animation does not work out of the box but that the MOL_animate and MOL_animate_frames nodes need to be added by hand. Off to more testing...

[@BradyJohnston]

Thanks for flagging this mate! Problem has now been fixed in 0.10.5: github.com/BradyAJohnston/MolecularNodes/releases/tag/v0.10.5

[@ByronHunter-r4h]

Hi Brady, thanks for the incredibly useful tools and tutorials! Was hoping you could help with a question. Using molecular nodes, is it possible to get the morph to pause for a certain number of frames (to highlight a specific conformation) before continuing? Thanks again.

[@maayaa77]

Do you know if cubesurfer is available or does Molecular talk to Geometry nodes for remeshing particle surfaces ?

[@the_bioway]

How to make a morph-file of ATP synthase using ChimeraX and exporting it into a multi-model PDB file...? You mentioned about that but I am unable to find it in description. Could you please share that one too. And as always Thanks a ton for these incredible tutorials

[@BradyJohnston]

You are correct, my apologies! I have added it to the description, and you can find the example here: bradyajohnston.github.io/MolecularNodes/examples.html

[@the_bioway]

@@BradyJohnston Brady, the given example link is not working anymore. Could you please share the working one please

[@AS-pu5wv]

I'm using the latest version of Mol Nodes with Blender 3.5, options have changed, and I can't get the ATP synthase to animate. Any chance of an explanation of how to update this video's instructions to the latest version?

[@SystemUpdate310]

Hi there, thank you for your work, it's an immensely useful plugin! I'm not very familiar with the molecular biology tools, so this might come off as a dumb question, but how do I see on the PDB site which protein file contains multiple frames? So it can be animated?

[@BradyJohnston]

Most structures will only contain one frame. Structures that were solved via NMR as a technique will contain multiple frames, so you can use NMR as a key word or filter by experimental technique to get structures that have multiple conformations in the one file.

[@SystemUpdate310]

@@BradyJohnston Awesome! Thanks for the fast reply.

[@SystemUpdate310]

​@@BradyJohnston Hi Brady! I hope you are having a wonderful day, sorry for bothering you again, just a quick question: What if I want to display just amino acids: let's say a proline molecule for example? I guess these are too simple to have articles and models of them on the PDB site. What is the most efficient way to have them in Blender? Thanks for your help.

[@simonojai]

Hi, great job, thank you for the video. How can we obtain the protein_frames file with an alphafold protein prediction ? I try to animate my protein but there is not frames file associated with it.

[@BradyJohnston]

If it is a multi-state pdb file, then Molecular Nodes should create the collection automatically. If you are wanting to create a multi-state pdb file, you can open multiple models from the alpha-fold prediction inside of pymol and then save it a as a single PDB file. If you find there there might be some kind of error, you can file a bug report here: github.com/BradyAJohnston/MolecularNodes/issues

[@westleyvanzant]

Incredible series! If using molecular nodes to generate visuals in a published work, do you ask for any specific citation? Thanks!

[@BradyJohnston]

Thanks! There is a DOI on the github via Zenodo, but I haven't gotten around to publishing anything yet!

[@shortfilmstudios4715]

Nice, but what can they be used for

[@GTS00000]

hey mate, are you deprecating all these functions? What are your plans for these tutorials if half of the stuff gets removed from mol nodes?

[@BradyJohnston]

Hello! The general idea behind the nodes is staying the same, but yes some of the functions are changing / being deprececated. I will be making some more tutorials to replace these (now outdated) ones, but I haven't found the time yet. I also want to wait until Blender 3.5 is our as there are a number of changes to GN coming in that version which I think would be important to highlight.

[@GTS00000]

​@@BradyJohnston Thanks for the detailed feedback. At the moment my main gripe is with M1 Macs. For whatever reason the new MN version isn't running properly and I had to switch to a Windows box in order to keep using it. Any idea when the Blender is being released? Keep it up! You are a hero!

[@BradyJohnston]

@@GTS00000 Blender 3.5 should be in a month or two I believe. M1 macs are proving problematic, but there is a workaround on the installation page: bradyajohnston.github.io/MolecularNodes/installation.html#installing-biotite-mdanalysis

[@GTS00000]

@@BradyJohnston I tried the workoround. Mac freezes for 30 seconds indeed. But nothing changes.

[@BradyJohnston]

@@GTS00000 if you can open an issue or comment on one of the open issues on github with more details, myself or somebody else might be able to help or we can work on creating a fix :)

[@GURMEETSINGH-ke1xc]

I couldn't able to install molecular nodes can anybody help me?

[@edgardoplasencia4208]

try installing from disk

[@Dr.R.]

I paid 8€ for an addon i hoped that it would do, what your addon does for free, this is so great. but the name was confusing ( i thought it would be the particel molecular script addon).... anyway, i am glad i found it and i am trying this it out right now... and it works great, so i bought you a coffee...

[@covalspace8191]

please use timestamps

[@brunoriyuoficial]

Good