Tutorial: Style your protein in Blender (in under 10 minutes)

This tutorial is made in Blender 3.0, but also works in older versions.
The protein I used is pdb 4JJ0 (Crystal structure of MamP): www.rcsb.org/structure/4jj0
The coordinate file was prepared in Yasara, but you can use any other software that is on hand. If you are new to importing poteins into Blender, here are some beginner’s tutorials for you:
Loading a Biomolecule from Chimera into Blender: • Biochemistry L3: Loadi...
Loading a Biomolecule from Yasara into Blender: • Biochemistry L4: Loadi...
Loading a Biomolecule from PyMol into Blender: • Biochemistry L5: Loadi...
00:00 Intro
00:10 Set up the scene
00:31 Import protein structure
01:34 Render "before reference"
01:55 Styling part, choosing shaders and adjusting them
03:38 Set up the lighting
04:33 Set up the background
05:21 Set up the "dust particles"
08:28 Camera settings (depth of field)
09:22 Render and final outcome
If you want a more detailed start with Blender, I would highly recommend starting with the tutorials created by Andrew Price: / andrewpp. .
Other resources for chemistry and biochemistry related content for Blender:
CG Figures: th-cam.com/channels/k1j.html...
Brady Johnston: / mrpiickles

[@mrhansenable]

amazing videos

[@LuminousLab]

Thanks :)

[@tomscheidt6758]

totally amazing I am your biggest fan

[@MarkUseBlender00]

nice

[@mrhansenable]

is it possible to color the molecules differently, or is it only done by atom? I am exporting from Chimera as Collada. My protein has two distinct molecules (ATP and NADH) which I'd like to distinguish through colors.
Also, I'm having a bit of a hard time with hydrogens. I'd like to display just the hydrogens on my ligand, but if I try to group by material for hydrogens it selects the entirety of the molecule. I guess I could simply delete the hydrogens in my entire molecule except for the ones I want to stylize.
Thanks again! I'm defending my thesis in a few months and plan to make some great visuals for my dissertation talk.

[@LuminousLab]

First of all: All the best already for your dissertation talk :)
Concerning your questions:
@Hydrgens: A you already said, preparing them in Chimera is definitely easier than deleting them afterwards in Blender.
The reason why the selection by material is not working here, it because the structural elements do have the same color as the hydrogen. You could also try to give your structural elements or the hydrogens a different color in Chimera (just an idea, I have not tried that ;) )
@Colors: Here you have two options:
1. You take care of the colors already in Chimera. If that does not help go for the following option.
2. Changing the colors in blender also works, but involves selecting the atoms separately. That can be nasty if you have large molecules (for NADH I would say it is fine). I talk about that a bit in the "Chimera to Blender tutorial" (th-cam.com/video/yllo0dwUVlM/w-d-xo.html starting @ min 14:46).
If you want to do it in Blender, I would go for the following workflow:
a) Select all atoms that keep the same color by their material (I assume that would be everything except carbon) and join them.
b) Hand-select the carbons that should be colored differently (from the smaller molecule) and join them and give them a different material.
c) Select the rest of the carbons by their material and join them.
d) Select the structural elements and give them a different material.
e) Rename all your materials so that you know which atoms/molecule they belong to and join everything.

[@mrhansenable]

@@LuminousLab you're great, thank you. watching your other videos now.

[@saraheidari2642]

Hello, i still don't know how to find that structure; what should i do with pbd and mamp?
Thank you for answering, i'm not familiar with data banks yet:(

[@LuminousLab]

Hi, the file was prepared using Yasara. There are tutorials linked in the description on how to use supporting software (like Yasara, Chimera, PyMol) to prepare a pdb file for import into Blender. I hope that helps.

[@sevetse949]

Can anybody tell which es the extension of the file imported trough Wavefront? As a pdf file cannot be imported. Thank you very much for any help.

[@LuminousLab]

I explain it here: th-cam.com/video/IJvX2jzZ3H4/w-d-xo.html (the supporting software in this case is Yasara). But you can also use PyMol or Chimera. Tutorials are linked in the description.
A pdf file cannot be important indeed. I assume you mean pdb file?

[@sevetse949]

@@LuminousLab Sorry, typing error, is pdb file not pdf !! I have also used Pymol to import a protein in its surface way, but the carbons are green instead of black. Thank you again

[@LuminousLab]

​@@sevetse949 To color the carbons (or atoms in general) to your preferred color, you need to change the settings of the material. In this video th-cam.com/video/5ZFVUej-bZs/w-d-xo.html at time stamp 4:23 I talk about regrouping and recoloring molecules imported from PyMol if no color is asigned at all. If you want, you can follow this method. If color is assigned to your atoms already, you can just change the settings in the material pannel.
As for the import problem with wavefront. It depends on the supporting software you use. Wavefront works best when exported from with Yasara, for Pymol I would recommend VRML(.wrl) for e.g. x3d for Chimera.

[@sevetse949]

@@LuminousLab Thank you very much for your answer. I follow the instructions of the video muy mention, but I could not paint the group joined, so I paint one by one. Perhaps depends of the version of Blender or I forgot a step. Anyway, thank you again