ChimeraX Protein Models in Blender | Blender for Biochemists

[@mayukhkansari4515]

yeah man keep posting more, these are really useful stuff

[@BradyJohnston]

Thanks for the encouragement! Will do!

[@K1LLC0]

YEEUSSSS!! You're back! Your tutorials are super useful. On my final year of biomedical science and I've been making animations and graphics to replace my professors lame and sometimes wrong ones they get from KZbin. Keep em up :D

[@BradyJohnston]

Glad they are helpful! More to come!

[@Clockworkbio]

Oh heck yes. I've been trying to work out a way to stop animating in 2d--and this gives me a lot to chew on. I kept hitting a wall in pymol and direct importing pdb files into houdini. It's NUTS how easy vertex color makes rendering the proper atomic colors in blender. Thanks so much for this--it's also super cool to see more folks from WA on youtube. Keep killing it!

[@BradyJohnston]

Glad I could help out! I've had that same struggle for so long. When I finally figured it out though - it changed everything! Ya'll have an awesome channel as well! Subscribed! If you need any help with trying to get stuff working in Blender just hit me up :)

[@axis3d]

Thank you for this primer. I'm still learning Blender (I'm a 30 year user of another 3D app), but this helps enormously with understanding the workflow between ChimeraX and Blender. Thanks!

[@malandr1]

The King have returned ! Please MOAAAR !! (and more frequently if possible '^^ )

[@BradyJohnston]

haha glad to be back! definitely more to come!

[@jondavid3564]

Excellent! Very informative. Thank you for sharing this tutorial.

[@ghoxon8312]

This doesn't have enough views. Incredibly useful, thank you!

[@BradyJohnston]

Glad it was helpful!

[@toddlawrimore3577]

Thank you. The .gltf format was unknown to me before this video.

[@SrgicalPrecision]

Amazing! Never new you could do this

[@massimilianoleoni7314]

I was looking to solve the exact same problem, thanks for this fantastic tutorial! Looking forward to watching the other videos in your channel shortly :D

[@drbonus]

Thanks for the video; the geometries are really waaaaaay better when exported from ChimeraX.

[@BradyJohnston]

Yep it makes a big difference!

[@christinecheng7800]

Thank you so much for uploading these videos! I've been trying to pursue a career in biomedical science and your videos have been really helpful.

[@BradyJohnston]

I'm glad they are helpful! More videos on the way! (exporting now...)

[@peter-xo3wx]

Fantastic tutorial！👀 Expect more about how to make great model and map rendering in blender.😃

[@matteocagiada2347]

Thanks Brady, really useful! I started using blender thanks to your videos and I think they are really useful for begginers. I am also a Chimera user, but I will probably upgrade to the X after this.

[@BradyJohnston]

Hi Matteo! Thanks for the kind words - and glad to hear that the videos are useful. Let me know if there is anything in particular you would like to see :)

[@Art-Science]

This is a great tutorial Brady!! Thanks you so much. Saved me a lot of time!!!

[@dkastner]

Sweet! The series continues!

[@BradyJohnston]

Thanks mate! Definitely more to come :)

[@lebenin3604]

This is great. Thank you. #blender #3d #3dmedial #medicalanimation

[@pungavaD]

Great tutorial. I had tried the previous ones, going to try this out too..

[@BradyJohnston]

Let me know how you go!

[@dnharry88]

Waitin... over! Thank you!

[@BradyJohnston]

I'm back!

[@fredhystair5789]

Hi Brady I just discovered your amazing work. That's really great. One question, on this tut. Can you access the vertex color property somewhere so that you can modifiy it ?

[@carolinestone4873]

This is fantastic, thank you so much for sharing!

[@BradyJohnston]

Thanks for the kind words! More to come :)

[@blenderzone5446]

thanks for sharing mate!

[@BradyJohnston]

Thanks!

[@blenderzone5446]

my pleasure!

[@MrOmid1955]

Nice video. Thanks for sharing.

[@the_bioway]

Superb! Keep it up🙌🏼

[@BradyJohnston]

Thank you! Will do!

[@user-hs3dg8jy3t]

Awesome video buddy! What specs are the pc running?

[@mrhansenable]

hey Brady, thanks for the tutorials. I'm trying to load large PDBs with multiple protomers into blender. They are in ribbon licorice style. When I load it just makes blender go so unbelievably slow, wondering if there's any way to help reduce the level of processing required? The only way I can figure out to show my molecules is to use molmap to get surfaces and import those. There's gotta be some trick here, because I see people rendering full cities yet I can't render a few blobs of licorice.

[@herbst7588]

Hey thank you for this! Very inspirational. I try to recreate it with my protein but when I search for the vertex color in the shader option, blender doesnt find it. Are there version differences? I cannot find it by using google.

[@BradyJohnston]

Thanks for mentioning this! Seems like there has been a change. Try the 'Color Attribute' node and you should be able to select the vertex color inside of there. Might have to do an update. I would recommend also looking into Molecular Nodes, I have greatly improve the import into Blender through my own addon: kzbin.info/www/bejne/eafQd5SIi9KNiLc

[@PaulEmsley]

Not heard of glTF... until now :-) Sounds useful, maybe assimp will make it easy to export.

[@BradyJohnston]

Yeah I hadn't really come across it until poking around in ChimeraX. Seems to be working really well!

[@dans5055]

I seem to be hitting a wall at the Vertex Colour section - I can't seem to pull up the node. Anyone else had issues with this? Thanks!

[@techdrums4204]

Brady, this is fantastic! Thanks for taking the time to make these tutorials. The biochemists community is small but passionate and I hope you get many likes and subscribers to keep you motivated to continue to make this content. One question. There seems to be an option to directly import a PDB file into blender. Is it not possible to work with that file and skip using either Chimera or Pymol? Cheers mate!

[@BradyJohnston]

Hi Sam! Thanks for the kind words! You are right that there is _limited_ functionality in Blender to directly import .pdb files. This import option only deals with atoms / sticks representation - not cartoon or surface. I've also found it to be kind of buggy and the sticks never work for me - so I basically gave up using it. I was going to cover that plugin and also the uPy ePMV plugin as well (which is similarly buggy, and only released for 2.80 on Windows).

[@rajivxxx]

Thanks for the video. Can you tell us how do make the background white & keep the shadow?

[@BradyJohnston]

Sure! In the render tab, there is a "film" section where you can tick the "transparent" option. That will render without any background, and you can add in the background colour of your choice. See here: docs.blender.org/manual/en/latest/render/cycles/render_settings/film.html

[@ScientistDjigr]

Hi! Apparently, as of January 2022 at least, .OBJ exports do work with cartoons. Do you think the colour information can still be retrieved with this format? In all cases, thank you so much for your videos, they are so useful!

[@wafiakbar3408]

Hi there, vertex colour has been removed in the current version of blender is there another way of doing this step?

[@刹那-l6k]

What key did you press to render the picture? I press F12 but Blender is not rendering. Instead, it only showed a picture like a screenshot.

[@gammaray0wn]

Awesome thanks

[@BradyJohnston]

No problem! More to come!

[@zzziii-qr5io]

cant find vertex colour

[@christinathompson5194]

what a great video ✔️✔️

[@BradyJohnston]

Thanks for the kind words :)

[@sciillu-scientificillustra4997]

Thank you so much for this tutorial. Is there a way to export the colors of the ribbon ? I've change some residues color in chimeraX, I would like to identify them into Blender. Thank you again !!

[@BradyJohnston]

Hello! If the colours are set in ChimeraX on the ribbon, then you can use the Vertex Colours that I show in this video and it should work

[@sciillu-scientificillustra4997]

Finally, I use the textureColors option when saving and it works. Thanks again 😀

[@dkastner]

Is there a way to add different textures to the colors? For example, if I want to make all the oxygens metallic. I used to use the Collada file type in Chimera which saved the colors as textures and you could edit them in blender. I'm bummed chimeraX doesn't have this output option

[@BradyJohnston]

I haven't played around with different textures other than different colours for atoms (using vertex colours). You could potentially "mask" using the vertex colours to get into different materials, but that starts getting into very complex shader setups very quickly so I don't know if it would be worth it. Sorry I can't be of more help! But I'll try and look into it for a future vide

[@cesargarciadiaz3738]

Thanks a lot :)

[@BradyJohnston]

You're welcome!

[@danielmorettimontoya4205]

How do I select single atoms, once imported in Blender?

[@BradyJohnston]

Hard to do so once inside of blender. Try making the selections in side of ChimeraX and then exporting to a different object, will likely be a lot easier!

[@pseudophd1073]

Good stuff, maybe it's time for me to abandon PyMol

[@BradyJohnston]

Yep I recommend taking the plunge! ChimeraX seems to doing a lot more exciting things compared to PyMol!