In molecular modeling, presenting a complex mechanism often requires temporarily hiding parts of a molecular system to direct attention. For example, a protein’s active site might be buried deep within a folded structure. To highlight its dynamics, it helps to hide surrounding residues before revealing the pocket. This seemingly minor task—removing clutter from a viewer’s perspective—can make your presentation more understandable and engaging. But how do you do that gracefully?
Enter the Hide animation in SAMSON. This tool lets you control node visibility using keyframes, making it possible to structure your story without permanently deleting or fading anything. The best part? It doesn’t touch transparency. Instead, it uses visibility toggling.
What really happens when you hide something?
The Hide animation is not just a visual trick. It works by ensuring selected nodes (like atoms, residues, or entire molecules) are visible up to a certain frame, and then instantly hidden from that frame onwards.
The animation has three keyframes by default:
- Between keyframes 1 and 2: the target nodes remain visible
- At keyframe 2: the nodes disappear
- Between keyframes 2 and 3: the nodes stay hidden
You can move these keyframes to adjust exactly when and for how long components disappear from your animation. This is perfect for synchronizing with other events in your sequence or highlighting structural transitions with clarity.
Use case: Explaining enzyme behavior
Say you’re presenting an enzyme’s catalytic mechanism. Initially, you might want to show the whole protein, then zoom in on the active site as the substrate approaches. Here’s how you can do that:
- Choose the surrounding residues (e.g., side chains not crucial to the mechanism).
- Open the Animation panel in the Animator.
- Double-click the Hide animation effect.
- Adjust the three keyframes to determine the visibility timeline.
In this way, you draw the viewer’s eye to the mechanistic detail, without forcing them to interpret a crowded scene.
Why not just delete or hide manually?
Manual hiding might interrupt the flow of your animation or require duplicated nodes. The Hide animation gives you smoother control, with visibility changes happening exactly when you decide. And unlike transparency effects, there’s no visual clutter—hidden nodes simply aren’t rendered.
Tip: Combine with ‘Show’
Hide isn’t always a solo act. Paired with the Show animation, it enables toggling visibility across different regions or models throughout your scene. Together, they give you clean control over what’s in view.
A note about the interface
Some older tutorials may mention an “Animation menu,” but this is no longer available. All animations can now be added from the Animation panel in the Animator workspace.
To learn more and see the full details, visit the original documentation page about the Hide animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download them at https://www.samson-connect.net.