When preparing molecular animations to communicate your findings—whether in academic presentations, lectures, or research videos—clarity is essential. A common challenge faced by molecular modelers is how to gradually remove part of a complex molecular structure without overwhelming visual transitions or ambiguous fading effects.
In SAMSON, a powerful platform for integrative molecular design, one handy solution to this challenge is the Hidden animation. This animation allows you to make specific molecular elements (or nodes) invisible between two keyframes—not by changing their transparency, but by toggling their actual visibility. This results in a cleaner transition for viewers and avoids clutter in the visualization.
When and Why to Use the Hidden Animation
Suppose you’re visualizing a protein-ligand interaction and, after introducing the binding site, you want to hide solvent molecules or secondary structural elements to zoom in on the region of interest. Rather than morphing or adjusting opacities, which can be visually unclear, you can precisely control the appearance and disappearance of groups of atoms with the Hidden animation.
How to Add a Hidden Animation in SAMSON
To add this effect, follow these simple steps:
- Select the nodes you want to make invisible.
- Open the Animation panel in the Animator interface.
- Double-click on the Hidden animation effect. This inserts a keyframe at your current frame, initiating the hidden transition.
- Adjust the keyframes to control precisely when the objects become hidden and reappear if needed.
Note: You can alter the interpolation of visibility using an Easing curve to fine-tune the pace of the transition.
What Makes It Different From Transparency
While both transparency and visibility can reduce visual load, the Hidden animation is true removal from view. Transparency often still shows outlines and makes dense molecular scenes cluttered. Hidden actually removes those objects visually, improving focus and reducing explanation time for your audience.
Before and After: A Visual Example
The following animation compares the Shown and Hidden effects on molecular parts as they are revealed or removed across keyframes:
This approach is particularly useful in dense systems like protein-ligand complexes, molecular dynamics trajectories, or supramolecular assemblies, where step-by-step clarity is key to interpretation.
To learn more about the Hidden animation and related features, visit the full documentation: https://documentation.samson-connect.net/users/latest/animations/hidden/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON here: https://www.samson-connect.net.