Creating compelling molecular presentations isn’t just about pretty graphics — it’s about telling a story. Molecular modelers often struggle with managing the visibility of atoms, molecules or entire structures over time, especially during animated timelines where some structures need to appear at specific key moments.
If you’ve ever wished you could just reveal a structure at just the right point in your molecular animation — and keep it visible as the scene moves forward — then the Show animation effect in SAMSON might save you a lot of unnecessary work.
Why visibility timing matters
When building molecular presentations, clarity is crucial: introducing structural elements too soon can add noise, while introducing them too late can result in lost context. To manage this, researchers often resort to manually hiding and showing molecular nodes across multiple keyframes — a task that can take considerable time and lead to inconsistent results.
This is exactly where SAMSON’s Show animation comes in: it provides a simple, visual way to make molecular nodes appear at just the right moment, and remain visible for the rest of the animation.
How it works
The Show animation is basically a shortcut: instead of setting up separate “hidden” and “shown” animations, the Show effect combines both processes in a single step.
Here’s what happens across its three keyframes:
- Keyframes 1 to 2: your selected nodes are hidden
- Keyframe 2: the nodes appear
- Keyframes 2 to 3: the nodes stay visible
This timeline allows you to control exactly when objects are introduced in your visualization — such as a ligand docking into a receptor, a conformational transition, or a key residue entering into a mechanism.
How to use it
1. In SAMSON, select the molecular nodes you want to show.
2. In the Animation panel, double-click the Show animation effect.
3. The 3 keyframes will be added to your timeline. Move them as needed to control when visibility transitions occur.
Note: You can always adjust keyframes after adding the animation to fine tune your presentation.
Customize transitions
By default, the appearance of nodes is abrupt. However, if you’d like to control how smoothly the transition between hidden and shown occurs (e.g., a slow fade-in), you can use the Easing curve to customize interpolation between frames. While this doesn’t affect node visibility directly, it allows for consistency with other animation timing in your scene.
Example
This simple animation illustrates what happens when you apply the Show animation to a node:
Using well-timed Show animations throughout your SAMSON projects can significantly boost the clarity and impact of your molecular stories.
To learn more about the Show animation and its use, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/show/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.