Appreciate that! Hopefully lots more to come :)

Coming soon! Lots in the works :)

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 :)

Hopefully it helps you keep making cool stuff!

thanks so much mate! hopefully you can put it to good use :)

@@BradyJohnston Already have!

Glad it helped! And I'm glad the tutorials are clear to follow :)

Thank you so much!

Thanks! Will do!

Thank you!

Thanks so much! Glad it is useful!

Thanks mate!

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)..

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.

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.

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!

Node wrangler! Learn all about it here: kzfaq.info/get/bejne/aeCqZcVqs6zVcmQ.html

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 (kzfaq.info/get/bejne/qNuqpbRn2rHadIU.html&)

@@BradyJohnston Thank you very much Brady. Great work.

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: kzfaq.info/get/bejne/ecybnaWgtMfbYJs.html

@@BradyJohnston Thanks! This tutorial was pretty useful. Godspeed on your future videos / projects good man.

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

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

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: kzfaq.info/get/bejne/ecybnaWgtMfbYJs.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.

working on it! lots of things to do and not a lot of time to do them

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