In this short tutorial, learn how to use the protein data bank plugin to create 3D protein structures.
The protein data bank plugin is integrated into BioRender and allows you to customize the 3D protein view to create stunning illustrations (0:05). Start creating your protein by inserting the PBD ID (0:20). Next, Shiz shows you how to rotate and re-color your protein (0:50). Layer the ribbon model on top of the space-filling model to create depth (2:11).
Meet the expert:
Shiz Aoki, CEO and co-founder of BioRender, shares her 10+ years of expertise as a distinguished science illustrator to help you bring your science to life - visually.
In this video, we're going to show you how to use the PDB plugin in BioRender and specifically how to layer the ribbon structure with the space fill model to create some nice depth in your illustration.
So I'm going to open up the PDB plugin here in BioRender. It's just the little tab here called PDB, and I'm going to click this blue button that says “create protein”. Now I know that the PDB ID I'm looking for is 6VW1.
So I'll type that in: 6VW1. Now to find this, you can go to the PDB website and search the protein that you're looking for and look for that specific alphanumeric. I'm going to click load protein. And I'm going to be able to rotate and re-color this protein as needed. I've got some beautiful shades and lighting options here for the proteins - a little bit more comprehensive than what's available on the PDB website.
We also have different imaging modalities. We've got quick surface, of course the ball and stick. So you can kind of select what you like there. I'm going to start with the cartoon model and rotate it to the angle that I like. Color and style - I can actually color by molecule, by chain, by sequence, and then perhaps uniformly across the whole molecule if I like. I can select a few of our predetermined colors in the drop down.
I think I'm going to select per molecule for this. I like that green and blue combo. Of course, I can change the border style and the shading style as well, cartoon versus flat. I'm going to stick with it for now and then save it as a new icon. So that's going to load up right onto my canvas and I'm not going to re-scale this.
I'm going to keep it as is just because what I'm going to do next is going to rely on matching up exactly the size 1:1. And this is that concept of layering the ribbon model on top of a space fill model to give it some depth.
I'm going to actually reopen this last PDB shape that I've created in BioRender. So if I double click this, It's going to reopen that PDB modal. I’m going to rotate it to exactly the angle that I made the last icon in.
So now any shape and size that I use is going to match exactly on top or behind that previous molecule. So I'm going to save this as a new icon. I can also change up the color a little bit if I want to change it up a little. Perhaps I'll give it a bit more of a 3D sort of toon shader look. And that looks pretty good to me. I'm going to save it as a new icon. I'm not going to overwrite the existing.
So you can see here that I've got two separate icons now, but if I drag this out, it should match up exactly 1:1 with the previous molecule. Now, what I might do is just nudge it a little bit bigger so that when I send it to the back, it'll match up nicely. And what I'm also going to do is actually select that background layer and decrease the opacity of that spacefill version. Again, that's going to create almost this sort of glass-like voluminous effect around that ribbon model. So you can see here it's kind of got that nice 1:1 match up. And now what I can do is resize it to my liking.
And what I might even do is have both selected, right-click and group it. It becomes a single icon that I've made custom. And that's how you use the PDB plugin in BioRender. We hope you try it out and let us know your thoughts.