Creating effective molecular animations often involves more than just showing atoms and molecules moving around. Sometimes, it’s just as important to hide elements at specific points—to guide attention, reduce clutter, or allow a progressive reveal of complex systems. If you’ve ever struggled with how to temporarily hide parts of your model without making them transparent, there’s a simple solution built into SAMSON: the “Hidden” animation effect.
Why hide instead of just fade?
Fading nodes using transparency can help in some cases, but it doesn’t remove them visually from the scene. Transparent atoms or molecules may still be partially visible and can distract from what’s being presented. The Hidden animation completely toggles a node’s visibility—meaning it’s either shown or not, with no in-between. This is especially useful when building step-by-step animations of molecular assemblies, reaction pathways, or binding site explorations.
Adding the ‘Hidden’ animation
To use this feature, start by selecting the nodes you want to hide during a portion of your animation. Then, open the Animation panel in the Animator and double-click on the Hidden effect. This inserts a keyframe that designates the starting point of the effect. You can adjust the position of keyframes to control how long the nodes remain hidden.
What’s especially convenient is that the Hidden animation uses the current time in the timeline to insert the first keyframe. This means you don’t have to set anything up manually beforehand—just move to the right time, apply the animation, and you’re good to go.
Customization: Easing Curves
Want to control how quickly or gradually the visibility changes between frames? You can adjust the Easing curve for the animation. This lets you fine-tune how the hidden status is interpolated over time, even though the transition is binary. While it may not seem immediately intuitive (since hiding is on/off), easing curves can still play a role when you’re synchronizing the ‘Hidden’ effect with other animations like movement or scaling.
Practical example: Building molecular narratives
Say you’re preparing a presentation where you want to first show a protein’s binding site and then gradually introduce surrounding molecules. You can use the ‘Shown’ animation on the binding site while using the ‘Hidden’ animation to temporarily switch off other components. Later in the animation, you can reverse it—’Show’ everything again to complete the scene. This kind of visibility choreography can clarify a story and significantly improve viewer understanding.
Note on the interface
Please be aware that animation effects are now managed from the Animation panel in the Animator. If you’ve used older versions of SAMSON, you may remember an Animation menu, but this is no longer present. You can now use convenient keyboard shortcuts too:
Ctrl + 7(on Windows/Linux)Cmd + 7(on macOS)
Refer to the original documentation to learn more about using the ‘Hidden’ animation, combining it with other effects like Appear, Pulse, or Show, and leveraging it in complex molecular scenarios.
SAMSON and all SAMSON Extensions are free for non-commercial use. To try it yourself, download SAMSON here.