When preparing molecular presentations, one common challenge is how to *introduce* a complex structure in an intuitive, scientifically accurate, and visually pleasing way. Whether you’re building a talk, creating a research video, or teaching protein assembly, it’s hard to beat a well-executed animation to communicate how molecular systems come together.
In SAMSON, the integrative molecular design platform, a simple yet effective animation effect — called Assemble — can help. With just a few clicks, you can show how your selected atoms or molecular fragments move towards their final positions, creating a clean, insightful visualization of molecular organization. This becomes especially powerful when explaining supramolecular assemblies or simply introducing large systems in a non-overwhelming way.
What the Assemble Animation Does
The Assemble animation in SAMSON makes a group of atoms or meshes appear as though they are assembling to their current positions over time. Starting positions are automatically generated away from final positions, which avoids overlap and creates a smooth visual transition that is ideal for presentations.
How to Add the Assemble Animation
Here’s a quick guide for applying this effect in SAMSON:
- Select the atoms, groups, or meshes to animate. If you don’t make a selection, SAMSON will try to infer what should be animated.
- In the Animator‘s Animation panel, double-click on the Assemble effect.
- Set keyframes to define how long the animation should take place.
Pro tip: While the initial motion amplitude is set automatically, you can fine-tune it using the Inspector panel. You can also adjust the easing curve to make the animation linear, ease-in, ease-out, etc., depending on your presentation style.
Why Use Assemble?
Imagine a scenario where you’re presenting a protein–ligand complex to an audience. Rather than starting with the complete and static structure, visually assembling the ligand into the pocket creates a natural buildup and facilitates storytelling — making the science more accessible.
This type of animation is also useful when comparing different states of an assembly, communicating docking results, or teaching about self-assembly in supramolecular chemistry or biological systems. It’s clean, non-distracting, and requires no scripting — almost instant results with high impact.
Example Output
Here’s an example of what the effect can look like in action:
For a quick video overview, you can also watch this 1-minute demonstration.
Use Cases in SAMSON Connect
You can explore real SAMSON documents using the Assemble animation such as:
This effect works hand-in-hand with others like Disassemble, Hold atoms, and Move atoms, giving you flexibility depending on your presentation goals.
To learn more, visit the official documentation page: 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.