Blender for Biochemists | Intro to Blender

[@Darkslide99]

This is the most practical Blender tutorial yet! perfect pace and i love the “use it as you need it” approach and it’s not overwhelming. thank you! I’m using Blender for Toxicology and i’m really struggling. this is perfect 👍🏽

[@nancydrew567]

cool ! I am also a toxicology researcher looking to use blender for animations to help others visualize my research

[@dkastner]

This is such an amazing series with so much potential! I don't know of anyone else sharing this type of blender content. Keep them coming!

[@BradyJohnston]

Thanks so much for your kind words mate, I will try to keep them coming!

[@erickoboo9654]

This is the most insightful tutorial, you been so helpful for me to learn skills in blender. Amazing work

[@christianorr5809]

Thanks so much for making this tutorial series, I've been waiting for something like this for ages! Looking forward to the rest!

[@koransumant6270]

god bless you for this tutorial, I never even conceived of combining blender's possibilities with protein models. Thank you so much!

[@MegaBulbs]

Came here from your series of reddit posts, im looking into getting in the field of scientific illustrations as a side hustle due to financial problems and these series are really helping me. Blender is not used by many in my field of pharmaceutical sciences and I hope to use it. Thank you

[@BradyJohnston]

Glad I can help out! It holds lots of potential for visualising science, so best of luck with it :)

[@nancydrew567]

What is the common platform used in pharmaceutical sciences?

[@PomboLiberdad]

I’ve been looking for blender tutorials specific to biology for such a long time, thank you for making this series!

[@BradyJohnston]

Thanks mate! I found myself in that situation a year ago, which is why that now I've gone through it the hard way I wanted to make it easier for others out there :)

[@jennyfromen2354]

This is awesome!! My sister asked me to make a cover image for one of her upcoming scientific journal articles, couldn't do it without your tutorial!! 👍👍👍

[@BradyJohnston]

Thanks for the kind words! You should check out my other tutorials for more proteins in Blender as well. Best of luck with the cover image!

[@swiftsword684]

I am a biochemist, currently, I am working on a video project regarding to biochemistry, thank you for your tutorial

[@jjgunt]

This amazing! Currently studying Pharmaceutical Biotechnology and I'm looking forward to playing around with this after finals :)

[@mayukhkansari4515]

Hi, really useful, looking forward more on blender and protein

[@j10001]

Simply phenomenal!! Thank you so much!

[@r.b.leveson-gower2166]

Great tutorial, thanks so much! Looking foward to the next ones

[@BradyJohnston]

Thanks for watching!

[@1400740]

Thanks a lot. Please do more and more science illustration videos

[@galacticbroadcastingcompan8756]

This looks very interesting. Thanks.

[@taforker]

Great tutorial! Look forward to see more :-)

[@KaplanAkincilar]

Really finding these tutorials helpful, thanks!

[@deepakanand5927]

thank you so much for sharing this.

[@filipaengrola1871]

Thank you very much for this tutorial, I've found it quite helpful!!!

[@carolinestone4873]

This is incredibly helpful; thank you for making this!

[@MrMonobody]

Thanks a lot Brady for this video, I learnt a lot! 👍

[@BradyJohnston]

Glad to hear it!

[@DJVARAO]

Finally what I was looking for! thanks so much

[@BradyJohnston]

Thanks! I'm trying to fill exactly that niche that I was looking for when I started out.

[@DJVARAO]

@@BradyJohnston Have you seen the covid tutorials? I am surprised virtually nobody got it right.

[@BradyJohnston]

@@DJVARAO Yeah I've seen some around, but they're all made by people who aren't structural biologists. I want to make my own series of building the coronavirus, but the PhD has a really bad habit of getting in the way of things unforunately.

[@DJVARAO]

@@BradyJohnston Hahaha I can totally understand. It is amazing you can spare some time for making videos. I agree, most illustrators are not familiar with the biochemical structure of the systems they do. I was trying to find a Cryo-EM capsid's structure of any of the SARS virus with no luck. So I think we only have the spike protein mostly. I bet anyone doing some fair model can get a publication out of it. I will be keeping an eye on your future videos and good luck with your research.

[@CraigDaly]

Thanks for this. I’m coming from Maya to Blender to do some molecular imaging, so this was perfect. Thanks. C

[@justinlynn]

This is awesome :) Thanks heaps Brady!

[@BradyJohnston]

late reply - thanks so much mate!

[@MichaelLeightonsKarlyPilkboys]

This is brilliant, thank you so much for this!

[@easy-food-safety]

Good inspiration!!!!!!!!

[@moya_watching]

Wow, so helpful. Thank you

[@alvin4891]

AMAZING!

[@AishwaryShivgan55]

Really useful... keep the good work! Thanks a lot

[@BradyJohnston]

late reply - Thanks a lot!

[@DJVARAO]

You kept the cube!😁 well done

[@BradyJohnston]

I would never betray the default cube

[@DJVARAO]

@@BradyJohnston hahaha

[@scifunart1252]

Hello Brady, I have been looking for blender tutorial from last year to make such pretty images for my research work. And this is the best of so far of which I have seen and very detailed tutorial for beginners like me. Also, I have few questions- 1. to use this software Blender, does it always require a very good graphics card or 4Gb+ RAM machine (desktop/laptop)? 2. How big system can be rendered using this tool? (Eg. 100000+ atoms systems which would include water, proteins or multiple membranes) 3. Also can you comment on the module BioBlender? Is it different than the BioMol module?

[@BradyJohnston]

I'm glad that have been useful! Blender is optimised very well, so it will run on even the most basic of computers. You are limited by the size of the scene you can make (how many objects) by the hardware on your computer (mostly RAM). But even if you have a small amount of RAM, you can still use it but just work on smaller scenes with less geometry. The speed at which you can render will be affected by GPU / CPU, if you don' have a new / expensive setup - you will still be able to render, it will just take a lot longer (but it'll get there eventually!). I haven't tested exactly the capacity of blender in terms on number of atoms etc so I can't help you there (but so far it can handle a lot if you go about it the right way). I've tried out BioBlender before but it wasn't being supported for a few years so it wasn't any use. I think development has resumed on it again, but I haven't tried it out for a few years so I can't comment (and I don't know what the BioMol is).

[@Mraus121]

Incredible video! Would love to see some videos on utilizing blender models in Unity if that's ever been something you've worked on.

[@BradyJohnston]

(Very late comment) but I have only dipped my toes into unity (see: made a cube and light) so I can’t help much there. On the list of things to maybe try out in the future

[@sergejkudruk8921]

Hey thank you very much for this amazing content! I would love to see more about membrane or nanocarrier modeling :) Cheers from Germany

[@BradyJohnston]

Thanks for the kind words! I have a video on membranes coming up. By nanocarries are you meaning kinesin and myosin? If so then yes I would love to cover them at some point!

[@uberfliege8289]

Ya answered my prayers...KUDOS and THANK you.

[@BradyJohnston]

I'm glad! Lots more videos to come!

[@周涛-w4w]

Thanks a lot for the fantastic sharing. I have a small question about the color of the proteins. Whether is it possible to color the protein with different colors for different helix or chains? like rainbow color...

[@BradyJohnston]

late reply - see my ChimeraX video. If you colour it inside ChimeraX and export from there you'll get the colours you are after :)

[@davidvargas5148]

Really good tutorial! Thank you so much for taking the time to show us how to work with this great program. I have a question, can you show us how to do this with proteins that have cofactors? Hb or something like? What about proteins that have metals?. Thank you so much! Looking forward to the next one

[@BradyJohnston]

You sure can! You can do it by showing the cofactors as spheres in pymol, then exporting them once they are visible. Using the BlendMol plugin from the Durrant Lab also works really well. I am going to do a video explaining that plugin soon as well.

[@PaulEmsley]

Very nice. Looking forward to the next ones. I'd like to see how you do electron density. /me googles VRML file format...

[@BradyJohnston]

Thanks Paul! Coot can export the electron densities as 3D files so we can import them into blender. I will add it to the list of topics to cover in coming tutorials :)

[@epgui]

I would be particularly interested in a video dedicated to materials and shaders with a focus on biochem.

[@BradyJohnston]

WIll add it to the list :)

[@meeodomodoeo4810]

Thank you in advance! two questions: can one have a transparent background? and how to install the BlendMol plugin?

[@younghope11]

Great video! May I ask have you tried with Macbook to do the 3D? Is that working well? And do you have any suggestions on which Macbook works fine? Thanks a lot!

[@BradyJohnston]

I have used my 2016 macbook for Blender and it does OK, but certainly not great. The newer M1 macs seem to perform very well, so I would recommend going for one of the M1 macbook pros if you can afford it. It will be cheaper to have a PC, but if you want to stick with mac then go M1.

[@younghope11]

@@BradyJohnston Thanks a lot for the suggestions and comments on M1. I do have a plan for M1, but not sure whether it perform better. Now I know the answer. Thanks again!

[@Thomaaasooo]

18:44 you really think a floating combination of red strings and helices next to a cube on a flat blue surface on a scale of maybe 10 nm is unrealistic? :D loved the vid btw. learnt a lot ;) i learnt a bit of Maya and used molecular maya to do some images but Maya is licensed so now i wanna learn blender for posters/papers. this vid was really straight forward.

[@BradyJohnston]

Thanks for the kind words! I started the same way with MolecularMaya (fantastic tool) but yeah it's a pity about the price of Maya licenses. Hopefully more to come of many Blender tips!

[@macwillson4098]

good stuff! where can I get my hands on a 3D DNA double helix!?

[@BradyJohnston]

Do you mean in real life or a 3D model? The pdb ID: 1BNA is a good double-helix model.

[@macwillson4098]

oh yes the 3D kind - thanks, so much. looking forward to more of your work, brother.

[@RachithSurana5500]

Great Job Brady. Subscribed . Is it possible to build blood brain barrier using blender? Thanks

[@BradyJohnston]

Thanks mate! One what sort of scale do you mean? Whatever you can think of, it's probably possible in blender. Do you mean on the molecular / mesoscopic scale, or large on a macro scale?

[@RachithSurana5500]

@@BradyJohnston Thank for the reply. Something like this www.google.co.in/url?sa=i&url=https%3A%2F%2Fwww.sciencephoto.com%2Fmedia%2F771720%2Fview%2Fblood-brain-barrier-illustration&psig=AOvVaw3QQGzHTIqrOzOtGm8zi-i4&ust=1606754037802000&source=images&cd=vfe&ved=0CAIQjRxqFwoTCNCXrq-XqO0CFQAAAAAdAAAAABAD

[@RachithSurana5500]

Or this www.google.co.in/url?sa=i&url=https%3A%2F%2Fwww.alamy.com%2Fstock-photo%2Fblood-brain-barrier.html&psig=AOvVaw3QQGzHTIqrOzOtGm8zi-i4&ust=1606754037802000&source=images&cd=vfe&ved=0CAIQjRxqFwoTCNCXrq-XqO0CFQAAAAAdAAAAABAI

[@kerolainebatista6028]

Hey. Do you use the paid version of paymol?

[@BradyJohnston]

nope I only use the free academic version

[@juliebachert4840]

This is great! Could you comment on why you chose Blender over other programs? I know that it’s open-source, but I think that many of those watching this video are academics, and several competing programs (Maya, Cinema4D, 3DS max) offer free academic licenses, and many institutions have subscriptions to those that don’t. Would you still go with Blender even if you had other options?

[@carolinestone4873]

I would also be very interested in the answer to this, as someone new to animation software.

[@BradyJohnston]

It's a great question, I listed a few things here: twitter.com/bradyajohnston/status/1254608425687805952?s=20

[@meeodomodoeo4810]

how to increase the resultant image resolution?

[@ghoxon8312]

Hey, thanks for doing this. I've switched to chimera for exporting structures, because at least for surfaces it can maintain color information and for cartoons you can render them smooth (not having that ugly blockiness you can see up close). Does anyone know a way to get ball and stick representations into blender without losing the color information? I currently don't know of one.

[@BradyJohnston]

Sure do! Made a more recent video here to maintain that colour information :) kzbin.info/www/bejne/qHPFXqWih9-araM

[@ghoxon8312]

@@BradyJohnston hero

[@mayukhkansari4515]

How to render an image with more higher resolution?

[@BradyJohnston]

Hi mate! You can adjust the specific resolution of the outputted image in the "Output Settings" tab. Get more details on it here: docs.blender.org/manual/en/latest/render/output/settings.html

[@mayukhkansari4515]

@@BradyJohnston Thanks

[@vikashkumar-cr7ee]

Hi Brady, thanks for your informative videos. By any chance you can make a tutorial for dendritic structure as shown in kzbin.info/www/bejne/Z2m4pGekpN5psJo ?Many thanks in advance

[@claytonbrown7120]

Trump wants us to eat this