Presenting complex molecular mechanisms in a clear and engaging way can be difficult, especially when your model begins as a disordered set of atoms or fragments. One common pain point molecular modelers face is how to visually demonstrate how molecular components come together over time—especially in presentations, videos, or during scientific communication.
That’s where the Assemble animation in SAMSON comes in. This animation effect is designed to make molecular structures appear as if they are assembling themselves into organized forms, helping you highlight structure formation and spatial arrangements in a direct, visually intuitive way.
When Visualization Tells the Story
Being able to show how components organize can be especially useful in the following contexts:
- Illustrating complex formation or docking events
- Presenting self-assembly processes
- Explaining steps in molecular machine operation
- Creating educational content for classes or outreach
Instead of showing the final, static structure, you can use Assemble to animate convergence from ‘exploded views’ or arbitrary spatial arrangements into a logical, final conformation. This helps viewers understand both the overall structure and the process of formation.
Using the Assemble Animation in SAMSON
Here’s how you can quickly make use of the Assemble animation:
- Select the group of nodes or meshes you want to animate. If no selection is made, SAMSON will try to make a smart guess.
- Open the Animation Panel in the Animator by accessing Interface > Animator, or using the shortcuts Ctrl + 7 / Cmd + 7.
- Double-click the Assemble animation. SAMSON automatically computes how far the atoms will move and generates two keyframes.
- Adjust the position of these keyframes to time the animation precisely.
- Customize further: Inspect the animation to tweak the amplitude of motion or experiment with different easing curves to control how the movement evolves over time.
Tips for Better Presentations
- Position the structure manually in a dispersed state if you want more dramatic assembly effects.
- Pair Assemble animations with camera motion (orbit or zoom) to create more immersive experiences.
- Use the Assemble animation across multiple keyframe segments to build complex multi-step sequences.
Below is an example of an Assemble animation used in a video to show the convergence of molecular components:
Want to explore a working example? Check out these public documents on SAMSON Connect that include the Assemble animation:
To learn more and view additional details, visit the official Assemble animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.