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ATP synthase (protein) turntable animation

January 17, 2013
Rendered in Blender (BI rendering engine, with some compositing), based on an imported PDB (protein databank) file.

Rendered in Blender (BI rendering engine, with some compositing), based on an imported PDB (protein databank) file.

ATP synthase is protein embedded in the cell’s membrane, which is in charge of creating ATP – a small molecule which is sometimes called  “cellular fuel”.

Since it’s such an important protein with an interesting, complex structure, I decided to make it the star of a short turntable 3D animation in Blender.

Last time I rendered a complex molecule (DNA), I used Blender’s unbiased rendering engine, Cycles.
I love cycles, and use it often, enjoying it’s straightforward node based workflow, wonderful global illumination and caustics. But its realistic rendering has a high cost in render times (several minutes per frame on my humble machine for the DNA animation), so I decided to use Blender’s internal rendering engine instead.

This is what I came up with (watch in full HD 1080p to view properly):

And here’s how it was done:

Importing the protein structure

Creating protein structures in blender is really easy these days, thanks to the “Atomic Blender” PDB importer script which is now an integral part of blender (since version 2.6 if I’m not mistaken).

To get it to work you need to go to blender’s user preferences and turn atomic blender on:


Then you need to import the PDB (protein databank) file through this addon. PDB files can be browsed and downloaded for free through the RCSB Protein Databank website.

After you download your file, import it through the File –> Import –> Protein Data Bank (.pdb) menu.

Though this is enough to import a PDB file into blender, it doesn’t allow much customization of the generated structure. To change various parameters such as the type of geometry (NURBS vs. polygonal spheres), the radius of various atoms and some other stuff, you need the Atomic Blender – Utilities Panel, which is a separate addon. In the addon page you can find installation instructions.


If you go to edit mode or wireframe view, you’ll notice that the imported geometry is made of NURBS spheres, that are instanced via points (dupliverts).

In the latest version of the addon (1.5) these can be separated and converted into other types of geometry through the Atomic Blender Utilities panel, in edit mode only (for further info see the very end of this wiki here).

Materials, Lighting and compositing

So, after importing the model, it was time to do some shading and lighting to make it look more interesting than with the default options. I didn’t change too much, only some basic shader options (reduced the intensity to 0.5, the specular intensity to 0.4, and shader types to Lambert with Blin specular highlights, while leaving the default shader colors unchanged).

I added two light sources, a strong spot key light at the right side of the camera with desaturated yellowish light, and a fill sun lamp with a bit of blue.


So, this gave a rather bland and basic render result, but I used a combination of two filters (Sharpen and Sobel, added together using a Color mix node in the node editor, set to add) to give it a more stylized look.


This is the node setup that was used (click to view full size):


Animation and Rendering

Not much to specify here, I simply made the whole structure turn a full 360 degrees (around the Z axis) over 100 frames.
I rendered the whole thing as RGBA PNG images (with a transparent background).

Final Compositing in the Video Sequence Editor

So, since the turntable animation didn’t look interesting enough by itself, I wanted to add a slightly “sci-fi”, futuristic look to it.

So I designed a minimal sci-fi panel in photoshop, and added it as a background for the animation in Blender’s video sequence editor (VSE).


When running the animation I noticed that the molecule is turning a bit too fast, so I added a speed control effect (in the VSE menu: Add –> Effect Strip –> Speed control) and scaled the whole animation to 150 frames.

The backdrop was added above the animation’s image sequence, with a “Alpha under” blend option (selected through the options panel, “N” shortcut key).

And then all that was left was re-rendering it and creating a video file which can be uploaded to youtube.

So, I hope this little post explains the process of creating this video and might be of help to you biological illustrators out there.

Feel free to leave me any feedback and comments.



From → Blender

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