When creating molecular presentations, one common challenge for researchers and educators is how to depict the transformation from scattered molecules to a structured complex. Whether you’re preparing a video abstract, a talk, or an educational resource, showing a molecule self-organizing into its final structure can make your content more intuitive and engaging.
This is where Assemble, one of the animation effects available in SAMSON (Structural Atomistic Modeling Software Network), becomes useful. The Assemble animation is designed to transition selected atoms or meshes from automatically computed initial positions back to their current locations in 3D space, creating a clear visual of how structures come together.
What the Assemble Effect Does
The Assemble animation makes selected molecular components—or even abstract meshes—move from positions computed away from their final location and smoothly return to their actual location over time. This is particularly useful if you want to illustrate the self-assembly process in supramolecular chemistry, protein docking, or multi-component molecular systems.
Here’s an example of what that can look like:
Setting It Up
1. First, select the atoms or nodes that you want to behave as assembling parts. You can select structural nodes or higher-level meshes.
2. Open the Animator in SAMSON and locate the Animation panel.
3. Double-click on the Assemble animation. If you haven’t pre-selected anything, SAMSON will try to intelligently guess which parts to animate.
Once inserted, the animation will establish its starting point based on your current model setup and generate two keyframes automatically. These keyframes define the trajectory of the animation from the spread-out to the assembled state. You can adjust the animation speed and duration by moving these keyframes along the timeline.
Customizing the Motion
One of the key benefits of the Assemble animation is that it adapts to the structure’s complexity by computing the amplitude of motion when the animation is created. However, if you want a more dynamic or more subtle movement, you can edit this manually using the Inspector.
You can further customize the movement by modifying the animation’s easing curve, which controls how the animation interpolates between frames—linear, ease-in, bounce, and others are available to match your visual narrative style.
Why Use Animate-to-Assemble Visuals?
Beyond making presentations more engaging, these animated transitions can help communicate mechanism, order of interaction, or even thermodynamic principles. For example, when showing protein-ligand recognition, an Assemble effect visually hints at the spontaneous nature of binding, even if the animation is illustrative.
It also works well in didactic content, where students might find it hard to mentally picture the transition from parts to whole at the atomic scale.
Video Example
If you’re curious to see it in action, here’s a quick video example demonstrating Assemble in SAMSON:
Explore More
This animation works well alongside other SAMSON animations, like Disassemble, for reverse processes, or Hold atoms and Move atoms for selective motion. Each builds upon the same Animator framework, making them easy to combine.
To learn more about how to use the Assemble animation in SAMSON, read the full documentation here:
https://documentation.samson-connect.net/users/latest/animations/assemble/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.