One of the constant challenges faced by molecular modelers is simplifying complex molecular scenes for presentations or animations. Whether it’s to highlight a reaction site, declutter overlapping strands, or direct attention to a specific structure, controlling visibility is a key component of effective molecular storytelling.
In SAMSON, the Hide animation is designed exactly for this use case. Instead of adjusting transparency or manually toggling structures on and off, you can automate the disappearance (and reappearance) of molecular nodes in a controlled and reproducible way.
When and Why to Use the Hide Animation
Let’s say you’re presenting a phosphorylation process. You want your audience to focus on the active center before the reaction occurs, then introduce surrounding molecules gradually. Instead of manually toggling visibility, apply the Hide animation to supporting molecules early on, making them disappear at a specific frame, and keep the focus on just what matters.
The real utility of Hide is its ability to control when this disappearance happens, and to ensure it persists until the desired part of the animation. All without modifying transparency (which can be visually confusing when residues pile up).
How It Works
The Hide animation works through keyframes. Here’s how the process flows:
- Keyframe 1: The nodes are visible.
- Keyframe 2: The nodes disappear entirely.
- Keyframe 3: The nodes remain hidden.
To apply it:
- Select one or more nodes (atoms, residues, molecules, etc.).
- Double-click on the Hide animation in the Animation panel of the Animator.
- Move the keyframes as needed to match your scene timeline.
Unlike fade-ins or opacity changes which can clutter a scene with partial data, Hide makes things gone. This gives you full control over visual density, useful in crowded systems such as protein-ligand envelopes or multi-molecule interactions.
More Than a Disappearing Act
For advanced users, you can fine-tune how the transition feels by adjusting the Easing curve. This is especially useful for matching the pacing of narration or integrating with other animated effects.
It’s worth noting that this animation effectively bundles what would normally require two separate animations — one to show and another to hide — into a single, more convenient effect.
If you’ve used the older Animation menu in SAMSON before, note this has been replaced. Now, everything is accessible via the Animation panel within the Animator interface.
Want to declutter your next molecular animation? Start by making what doesn’t matter disappear — at just the right moment.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.