Hi.
My name is Janet Iwasa.
I'm in the Department of Biochemistry at the University of Utah, and today I'll be talking to you,
in this last of three videos, about molecular animation.
So, we'll be walking you through the animation process in the animation software,
and also talking about compositing.
So, one of the things that is important to note, and a lot of people ask me about,
is what software should they use.
So, there are a lot of different 3D animation packages out there.
And I think... my personal feeling is that you can create any animation, the same animation,
in any one of these packages.
It doesn't really matter too much which one you choose.
But there are differences in terms of the ease of learning, as well as the cost.
So, for example, Blender, the last one you see here, is a free and open-source package.
The one I'm going to be talking to you about, and the one I just happened to learn is Maya,
which is created by Autodesk.
But really, you can probably try downloading trial versions of any one of these softwares
and see which one you like the best.
So, just an overview of the animation process.
So, the first thing that we did, actually, already in the previous video, is we created geometry.
We created these model... molecular models.
And so in this process, now that we're in the animation software, we're going to import that geometry.
Then we're going to add some shading, texturing, and lighting to that, to the scene.
And then next we're going to animate it, which is to say move things around,
deform things if needed.
Things like that are done in the animation stage.
And then finally, we render out the images from the animation software.
And then we take it into the compositing software.
And in my situation... there's also different compositing software packages.
I'm most familiar with Adobe After Effects, so I'll be showing you how to do compositing there.
Alright.
So, let's jump into Maya.
In this video, I'll be providing a very brief overview of the animation process,
focusing specifically on some of the tools that are the most useful when thinking about
creating a molecular animation.
Although I'll be using Autodesk Maya here, this workflow, and most of the processes I'm showing,
can be done using any professional 3D animation program.
The general workflow looks like this.
First, we'll build our models.
This can be done by either importing molecular structures from software like Chimera,
like we showed in the last video, or they can be built within the 3D animation software.
Next, we animate the models.
There are a large number of tools in 3D animation programs to make things move,
and I'll be demonstrating a few different methods in this video.
In the next stage, we'll add different textures or shaders to the objects, and also set up
lights and a camera.
The animation is then rendered into a series of images or frames.
These images get imported into a compositing software that we can use to add things
like sound, labels, and some other effects.
Just one last thing to note: this is a really short video that provides a brief glimpse
into how to create an animation.
And I'll be moving pretty quickly through different steps.
If you're interested in trying out 3D animation, I encourage you to look into local courses
or free online tutorials that will allow you to really see every step in detail.
Okay.
So, let's get started.
At the end of the last video, we used Chimera to export a model of an actin filament
in a format called OBJ.
Now we're going to import that into our 3D animation software.
Structures are typically imported at sort of a large scale, at a random orientation,
and way off of center.
So, there's a little adjusting that needs to be done first so that it's easier to work with.
I'm going to scale the actin filament, and bring it to the center of the scene, and rotate it.
I've also created a group of all the actin monomers in the filament so I can move
the filament as one object.
The model also comes in with some textures already applied, which we're going to ignore
for the time being.
I'll also rename each monomer so that it's something that I can more easily read.
For this animation, I'd like to create a longer actin filament, so I'll duplicate this section
and rotate it so that it aligns with the previous section.
Then, we can repeat this command until the actin filament is as long as we'd like.
In some cases, where you don't have a structure to import, or maybe you only have
a partial structure, you can use some tools to create the full structure.
In this case, I've got a protein that has a long flexible domain that I'll need to model.
I'll create this flexible domain using a tool that allows me to extrude a cylinder-like shape
along a curve.
I'd also like to create a membrane for this animation.
First, I'll create a plane and bend it around a bit.
Then I'm going to use a fun tool that allows me to create some hair like things on it.
These hairs can be adjusted to look like little cylinders that I think can be a nice stand-in
for membrane lipids.
Okay.
So, now that we've built some models, it's time to start animating them.
Animation software comes with many different tools to create different types of movement,
and I'll be demonstrating just a few of them here.
The most basic type of animation is just keyframing movement.
For example, if I want to create an animation of an actin monomer binding
to the end of this actin filament, I can take the last monomer, and at the last frame of the animation
keyframe it into its final position in the filament.
Then I can move the current frame to the first frame and move the actin monomer
somewhere else and keyframe it.
Now, when I play the animation, the actin looks like it's moving to the end of the filament.
We can add a few more keyframes in the middle to add a bit more random movement too.
Say I'd like to make my actin filament bend or flex.
We could use a different tool to make this effect.
In Maya, they're called deformers, that can act on some geometry.
In this case, I'm using a bend deformer to make the actin filament bend back and forth.
Another way of animating bending or conformational changes is through using skeletons.
In this case, I'm creating a skeleton to control the bending of a flexible domain.
After making the skeleton, I attach it, or skin it, to a piece of geometry, in this case
the cylinder that I already created.
I can then set up a control for the end of the flexible domain so I can control its movement
easily using a handle.
Most animation software allows you to write scripts that you can use to animate scenes.
Maya uses a language called MEL that I often use to carry out repetitive tasks.
In this example, I'm using a short MEL script to keyframe the appearance of actin monomers
over time so it looks like the actin filament is growing.
This could have been done manually, but would have taken much longer than it did
to write these few lines of code.
I'm now going to focus on texturing or shading.
3D animation software typically has a separate panel that allows you to create different materials.
These can be shiny, bumpy, reflective, in different colors.
For molecular surfaces, I like to keep things simple, and just use a relatively smooth texture,
and use color to allow viewers to easily distinguish different proteins.
So, I'll make actin be a few different shades of green, and have this other protein be yellow,
and the membrane will be white.
3D animation software also includes a lot of different types of lights you can place in your scene.
For the purposes of this simple animation, I like to use just a simple lighting setup
that provides some good shadowing between different objects.
Now, you also have to set up a camera from which you'll be doing your rendering.
This camera can be animated to zoom in to a scene or to follow an object.
Finally, it's time to set up the render.
The animation software renders out each frame, one at a time.
And each frame typically only takes up a fraction of a second in the final movie.
In this last section of the video, we'll be using compositing software to take
the rendered frames of the animation to create a video.
There are different types of compositing software, and the one that I'll be using is called
Adobe After Effects.
Compositing software allows you to add effects or to adjust the animation in a similar way
that Photoshop allows you to adjust images.
You can also use compositing software to add text, such as titling or labeling,
and to adjust the timing of the video by speeding things up, slowing them down,
or adding still frames.
You can also add sound, such as a voiceover narration or music.
All of these elements are visible in a timeline, so you can see how long each element is, and
you can adjust them separately.
You can also use compositing software to create animations.
This can be done by adding effects on top of a frame that was rendered in 3D animation software,
like adding a sway to this actin filament, or by importing a 2D vector illustration,
as shown here, and adding motion to it.
Once you're done compositing, you can export the finished video.
So, now, hopefully, you have some familiarity with what the process looks like
inside the animation software and also that compositing step.
So, in this last slide, I really wanted to talk about more resources for learning more.
So, we were just able to really kind of cover kind of a basic level of what
the animation software can do.
And there's a lot more that you can learn on any one of these software packages.
The best way to look for... to learn more is to just go online and to look for
different tutorials and resources.
So, some of the best places to look for tutorials are actually from the manufacturers that
often provide various tutorials for free on their websites.
Again, you can take more structured courses online through sites like Lynda.com,
so that's also worth exploring.
But my favorite option for learning things, especially something very in-depth
like 3D animation software, is to try to take a local course if possible.
I think it just forces you to go through everything.
It provides you with an instructor who you can ask questions to.
So, if you're at a university, you should check your art department, your film department,
to see if they have courses available for 3D animation.
Thank you for watching.
I hope you enjoyed this series of three videos.