Being a Professor of Biochemistry I do believe this has some fantastic application in the field of teaching too! Incredible work and awesome tutorial Sir👏👏👏 Thank you!
This is absolutely incredible!! Thank you for doing this. We need more artist scientists willing to teach the rest of us. I can't wait for the next one!
Great video. To save rendering time for a final composition which features lots of proteins, render out 4 or 5 different views of an individual protein at low sampling so it gets done quick, then import those rendered pngs back into the project and put them into their own collection. Then instantiate the collection in a particle system and scatter as many proteins as you want without incapacitating your computer in the process.
It is really great that you have created these videos. Thanks so much. I have a question: When I import as you have from PyMOL, the surface and cartoon are basically colorless like is the case for you, but the cofactor in stick representation is still colored. As a result, the emission shader doesn't really do anything to it whereas is glows in yours. Do you know how I can either import without the color or remove the color that it is imported with?
depends on the method which you are exporting the object from PyMol as. PyMol may have changed how it exports stuff as well. You can assign the same material to all of the mesh, which sounds like it may fix your issue.
I do plan on making more! It has been a hectic time in my PhD but I should hopefully be putting some more out soon :) If you want something in particular covered, let me know and I will add it to my list! Also thanks for the comment, I do sometimes need the extra motivation to hurry up and make another video :)
Just wanted to say thanks for these uploads! I have known about blender for awhile but was often intimidated by the more niche design principles and the overwhelming amount of options presented to the user. Your videos help break it down in a context that is familiar so I greatest appreciate that! Looking forward to more content when you find the time🤞🏼
Hey Brady, fantastic videos, I think many folks adore it. I truly hope you could manage your move smoothly and we can expect you back! Best wishes mate!
Hi Brady, thanks for the awesome tutorials! Basic question: I imported a .wrl file, loaded as cylinder objects, and then joined using command+j. I see that the objects are joined together, but when I tried to apply the emission shader it only adds it to a single object, as opposed to all the cylinders in the group. Do you have any idea of what I'm doing wrong?
@@weca1022 So it turns out that the issue in my case was that each cylinder was being imported with its own unique material. I think something has changed in either PyMol/Blender since the time Brady recorded this. Anyways, to resolve this I had to delete all of the materials associated with the cylinder objects. My solution was to go to "Blender File" display mode (look for the button at the top right of the screen that looks like a stack of images), go down to the materials section, select all the materials corresponding to the cylinders, and then right click + delete. I did all of this *before* joining the objects. After that I could modify the shader properties of all the cylinders in the group together :). If anyone with lots of blender experience sees this: - Is there an easier way to delete multiple materials at once? What if you don't know their names? - If I delete the materials after joining the objects, then I have the same problem from before, where I can only edit the material properties of one cylinder at a time. It seems like after joining, each object gets its own "slot". Is there a way to delete those/reset them in bulk?
Sorry for my absence in replying! Seems you figure out partially what the problem is. I think I definitely need to re-record some newer and more up-to-date tutorials for the channel. Before you join the meshes with Ctrl+J, you can copy the material from one to all of the others with Ctrl+L and choose material. That will ensure they are all using the same material before you join them.
@@BradyJohnston My (pipe?)dream would be to get a loop-opening motion animated in Blender, and preferably while still displaying a transparent surface on top (I can hear my fans spinning up in anticipation). I have done this in pymol with a rigimol morph and good ol' ray, but the pymol ray-tracer leaves a somewhat blotchy mess. I imagine this is a pretty complex job, probably beyond your scope: but facets of this would still be cool!
@@BlakeTRiley if you could give me more details of what kind of loop opening you are after I could have a look, especially if you're already got an animated file setup in PyMol.
Glad you are enjoying them! Towards the end of 2020 I upgraded to this current build (pcpartpicker.com/user/bunchofbradys/builds/#view=Cr7XsY) but before that I had a much older PC for these initial videos.
Hey brady amazing videos loving the series so far please keep making these videos, i have always loved the idea of art but conventional art is not for me you have mixed my interest for art and passion for science, these videos have been so amazing and a much needed help in the right direction. Hope you will make more of these videos
Really cool! Thanks! Too bad PyMol license is very expensive. You know of any truly open source program that can generate this molecules to import on Blender?
loved this video, Brady. Would you please consider making a tutorial on how to import lammps data file into Blender for visualization. I can send you polymer data file if you want.
is it possible to merge vertices with a model rather than the surface? I have a few big models Ive loaded in and it's going so slow to do anything. Tried removing vertices but not working.
Do you ever get problems with bumpy beta strands? Short of adding a bunch of subdivision modifiers, I can't seem to find a way round it... Helices look fine
Thanks! Will hopefully be more soon, have had a busy time with PhD but wanting to make some more. If there is something in particular you want to see covered, let me know :)
@@BradyJohnston Sweet 😍! I'm a grad student in biochemistry and i've also been using blender for some time as a hobby, I've always been deeply interested by 3D molecular animation (cf. what Ribosome Studio and the like do). Have you noticed the addon Bioblender have been updated very recently? What I would like to see the most is a full work on a protein-ligand docking/enzymatic scene with completed shading, rigging, animation and camera job. That would be extremely helpful!
@@BradyJohnston I'm especially having a hard time at the turbulence animation part (dynamic animation of the protein structure, groups rotating, overall structure jiggling etc), it's easily done in maya with the addon mMaya or in Houdini but it seems a lot more complex in blender. Maybe a little python script could do the work
Thank you for the tutorial! I really liked your approach for smoothing the surfaces (I used to generate more smooth surfaces already in Chimera "e.g., Surface generation commands" - munfred.com/proteins.html ). As for the future tutorials, I wonder how do you fix 'stick representation' in Blender (like the inhibitor in this tutorial, the 'ball atoms' in the 'corners' clearly disappeared) and how do you color different parts of the molecules in different colors...
Thanks for the kind words! I have been playing around with ChimeraX (hadn't used it prior to making these videos) and it is definitely better for exporting geometry from than PyMol seems to be. I had a play around and a simple fix seems to be exporting the stick geometry from ChimeraX rather than PyMol. I'm going to be making my next video on exporting things from ChimeraX rather than PyMol which will also make cartoons and ribbon representation look a lot better as well.
Thanks mate! That's a good suggestion, I'll try out some different background colours. I also accidentally exported this video at a lower bit-rate so things are a bit more compressed than would be ideal. There are a lot of things to be aware of with this whole youtube thing.
Didn't notice any compression artefacts at all. I liked your picture in picture effect to engage audience when the subject ("what does this button do") gets a bit dry. I really enjoyed the background stuff with pymol too, thanks for that. I sometimes need to make bio-graphics for TV and its nice to see what corners can be cut and what should be left in. I guess it depends on the audience...
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Hi! Thanks for the tutorial! I was wondering how difficult (if possible) would it be to import a molecular dynamics trajectory into blender.
Glad you enjoyed it. It's very possible, a great addon I have tried is Pyrite (durrantlab.pitt.edu/pyrite/). I plan on doing a video tutorial on it sometime in the future :)
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@@BradyJohnston Coooool! By the way do you have a Patreon account?
@@KristenLee Will have more time to try and do some stuff in like 2 weeks, will definitely start recording more then if not before :) The jiggling will come!
Being a Professor of Biochemistry I do believe this has some fantastic application in the field of teaching too!
Incredible work and awesome tutorial Sir👏👏👏
Thank you!
Thanks for the kind words! I appreciate it, and hopefully there should be more to come soon!
This is absolutely incredible!! Thank you for doing this. We need more artist scientists willing to teach the rest of us. I can't wait for the next one!
Could you please make a video on Rigging and Animating the protein ? It would be of great help !
late reply - I will do ! In the pipeline :)
Great video. To save rendering time for a final composition which features lots of proteins, render out 4 or 5 different views of an individual protein at low sampling so it gets done quick, then import those rendered pngs back into the project and put them into their own collection. Then instantiate the collection in a particle system and scatter as many proteins as you want without incapacitating your computer in the process.
Yep this is a great approach! I have tried it out for larger scenes and will introduce it in a later video to help speed things up for people.
Fantastic art! Can’t wait to try it and show the results to my advisor.
It is really great that you have created these videos. Thanks so much. I have a question: When I import as you have from PyMOL, the surface and cartoon are basically colorless like is the case for you, but the cofactor in stick representation is still colored. As a result, the emission shader doesn't really do anything to it whereas is glows in yours. Do you know how I can either import without the color or remove the color that it is imported with?
depends on the method which you are exporting the object from PyMol as. PyMol may have changed how it exports stuff as well. You can assign the same material to all of the mesh, which sounds like it may fix your issue.
When I save a drug molecule in stick form as a wrl it is imported into blender with color. Do you know how to change this?
subbing for the slight chance you're gonna make more of these.... the idea of combining my passion for art and my biology degree is thrilling
I do plan on making more! It has been a hectic time in my PhD but I should hopefully be putting some more out soon :) If you want something in particular covered, let me know and I will add it to my list!
Also thanks for the comment, I do sometimes need the extra motivation to hurry up and make another video :)
Just wanted to say thanks for these uploads! I have known about blender for awhile but was often intimidated by the more niche design principles and the overwhelming amount of options presented to the user. Your videos help break it down in a context that is familiar so I greatest appreciate that! Looking forward to more content when you find the time🤞🏼
Sorry for the later reply, but thanks so much for the kind words! I'm glad they have been useful and I hope to make many more in the future!
Hey Brady, fantastic videos, I think many folks adore it. I truly hope you could manage your move smoothly and we can expect you back! Best wishes mate!
Very late reply (and have moved, yet again) but thanks for the kind words! Have made some more and definitely more to come :)
Thank you very much for this tutorial!!! Can't wait for the next one :)
Thanks so much! Hopefully I can make some more soon :) Sometimes I unfortunately have to continue working on my PhD ...
Hi Brady, thanks for the awesome tutorials! Basic question: I imported a .wrl file, loaded as cylinder objects, and then joined using command+j. I see that the objects are joined together, but when I tried to apply the emission shader it only adds it to a single object, as opposed to all the cylinders in the group. Do you have any idea of what I'm doing wrong?
I've got the same problem, can you lmk if you found a solution?
@@weca1022 So it turns out that the issue in my case was that each cylinder was being imported with its own unique material. I think something has changed in either PyMol/Blender since the time Brady recorded this. Anyways, to resolve this I had to delete all of the materials associated with the cylinder objects. My solution was to go to "Blender File" display mode (look for the button at the top right of the screen that looks like a stack of images), go down to the materials section, select all the materials corresponding to the cylinders, and then right click + delete. I did all of this *before* joining the objects. After that I could modify the shader properties of all the cylinders in the group together :).
If anyone with lots of blender experience sees this:
- Is there an easier way to delete multiple materials at once? What if you don't know their names?
- If I delete the materials after joining the objects, then I have the same problem from before, where I can only edit the material properties of one cylinder at a time. It seems like after joining, each object gets its own "slot". Is there a way to delete those/reset them in bulk?
Sorry for my absence in replying! Seems you figure out partially what the problem is. I think I definitely need to re-record some newer and more up-to-date tutorials for the channel.
Before you join the meshes with Ctrl+J, you can copy the material from one to all of the others with Ctrl+L and choose material. That will ensure they are all using the same material before you join them.
Fantastic! This was about as far as I'd managed to explore on my own, about two years ago. Can't wait to see what's coming next. :)
Thanks mate! Hopefully lots more to come, plenty of things to cover. If you have anything specifically you would like me to tackle let me know!
@@BradyJohnston My (pipe?)dream would be to get a loop-opening motion animated in Blender, and preferably while still displaying a transparent surface on top (I can hear my fans spinning up in anticipation).
I have done this in pymol with a rigimol morph and good ol' ray, but the pymol ray-tracer leaves a somewhat blotchy mess.
I imagine this is a pretty complex job, probably beyond your scope: but facets of this would still be cool!
@@BlakeTRiley if you could give me more details of what kind of loop opening you are after I could have a look, especially if you're already got an animated file setup in PyMol.
You’re amazing! Thank you!!
(Except for the glow) this composition is reminiscent of this week's cover of Nature
I thought it looked similar too! It's a common type of composition, I'm flattered to be compared to Nature :)
Please come back!
late reply - I'm back!
thank you for this. a lot of specific info here.
Thanks for creating and sharing the video! quite informative
Glad you liked it!
I'm very excited to be following along with these, thank you for making them available! May I ask, what specs does your computer have?
Glad you are enjoying them! Towards the end of 2020 I upgraded to this current build (pcpartpicker.com/user/bunchofbradys/builds/#view=Cr7XsY) but before that I had a much older PC for these initial videos.
@@BradyJohnston thank you!
Please do many many many more of these, with some rigging too! :)
Some rigging is on the list! I have just recently moved and will hopefully have some more time to make some new videos soon! Glad you liked them :)
Hey brady amazing videos loving the series so far please keep making these videos, i have always loved the idea of art but conventional art is not for me you have mixed my interest for art and passion for science, these videos have been so amazing and a much needed help in the right direction. Hope you will make more of these videos
Thanks mate! I too love the intersection of art and science. Very busy writing PhD thesis at the moment but hopefully some more videos soon
Really cool! Thanks! Too bad PyMol license is very expensive. You know of any truly open source program that can generate this molecules to import on Blender?
make more videos like this please
Good work. Please make more if you find the time :)
Late reply - thanks for the kind comment! Have finally started making more :)
loved this video, Brady. Would you please consider making a tutorial on how to import lammps data file into Blender for visualization. I can send you polymer data file if you want.
is it possible to merge vertices with a model rather than the surface? I have a few big models Ive loaded in and it's going so slow to do anything. Tried removing vertices but not working.
Amazing work!
late reply - thanks so much!
How to generate multiple random protein surfaces?
Do you ever get problems with bumpy beta strands? Short of adding a bunch of subdivision modifiers, I can't seem to find a way round it... Helices look fine
late reply - Exporting from ChimerX seems to improve the geometry a lot. See one of my latest videos :)
Please MOAR!!
Thanks! Will hopefully be more soon, have had a busy time with PhD but wanting to make some more. If there is something in particular you want to see covered, let me know :)
@@BradyJohnston Sweet 😍! I'm a grad student in biochemistry and i've also been using blender for some time as a hobby, I've always been deeply interested by 3D molecular animation (cf. what Ribosome Studio and the like do). Have you noticed the addon Bioblender have been updated very recently?
What I would like to see the most is a full work on a protein-ligand docking/enzymatic scene with completed shading, rigging, animation and camera job. That would be extremely helpful!
@@BradyJohnston I'm especially having a hard time at the turbulence animation part (dynamic animation of the protein structure, groups rotating, overall structure jiggling etc), it's easily done in maya with the addon mMaya or in Houdini but it seems a lot more complex in blender. Maybe a little python script could do the work
Thank you for the tutorial! I really liked your approach for smoothing the surfaces (I used to generate more smooth surfaces already in Chimera "e.g., Surface generation commands" - munfred.com/proteins.html ).
As for the future tutorials, I wonder how do you fix 'stick representation' in Blender (like the inhibitor in this tutorial, the 'ball atoms' in the 'corners' clearly disappeared) and how do you color different parts of the molecules in different colors...
Thanks for the kind words! I have been playing around with ChimeraX (hadn't used it prior to making these videos) and it is definitely better for exporting geometry from than PyMol seems to be.
I had a play around and a simple fix seems to be exporting the stick geometry from ChimeraX rather than PyMol. I'm going to be making my next video on exporting things from ChimeraX rather than PyMol which will also make cartoons and ribbon representation look a lot better as well.
I am not a biochemist but I think that it would be easier to see what you were achieving by altering the world colour away from grey. Great tut tho!
Thanks mate! That's a good suggestion, I'll try out some different background colours. I also accidentally exported this video at a lower bit-rate so things are a bit more compressed than would be ideal. There are a lot of things to be aware of with this whole youtube thing.
Didn't notice any compression artefacts at all. I liked your picture in picture effect to engage audience when the subject ("what does this button do") gets a bit dry. I really enjoyed the background stuff with pymol too, thanks for that. I sometimes need to make bio-graphics for TV and its nice to see what corners can be cut and what should be left in. I guess it depends on the audience...
Hi! Thanks for the tutorial! I was wondering how difficult (if possible) would it be to import a molecular dynamics trajectory into blender.
Glad you enjoyed it. It's very possible, a great addon I have tried is Pyrite (durrantlab.pitt.edu/pyrite/). I plan on doing a video tutorial on it sometime in the future :)
@@BradyJohnston Coooool! By the way do you have a Patreon account?
@ I do not! Wouldn't have even thought people would want to pay me for this kind of stuff.
@@BradyJohnston Hey Brady! Please please please do a tutorial on this soon. I'm struggling so much just to get it set up. I wanna see jiggling!
@@KristenLee Will have more time to try and do some stuff in like 2 weeks, will definitely start recording more then if not before :) The jiggling will come!
So, I will try not to add those weird things then.
I'm unsure what you mean by this?
@@BradyJohnston 10:39