When preparing scientific animations and presentations of molecular structures, one recurring challenge is managing visual complexity. Molecular modelers often need to control what parts of a structure remain visible to highlight others. A common pain point is the lack of flexibility in hiding structural elements only for specific timeframes in animations, without permanently altering the system or toggling transparency in non-intuitive ways.
The Hide animation in SAMSON provides a simple and effective solution. It makes selected nodes disappear visually at a given point in time (the second keyframe), and ensures they stay hidden for the rest of the animation until the final keyframe. This operation is done programmatically through visibility flags rather than transparency — meaning the objects are completely turned off, not just faded out.
Why not just use transparency?
While transparency is helpful in some contexts, it introduces visual clutter and often requires fine-tuning to keep the scene readable. With Hide, you ensure that components are cleanly removed when it matters most — for example, quickly focusing attention on a ligand binding site, removing the solvent for an enzyme mechanism, or sequentially hiding parts of a protein to follow a folding path.
How to use the Hide animation
Here’s how the Hide animation works in practice:
- Select the nodes you want to hide (e.g., sidechains, ligands, or entire subunits).
- In the Animation panel of the Animator, double-click on Hide.
- You’ll now have three keyframes:
- Keyframe 1–2: Elements are visible.
- At Keyframe 2: Selected elements are hidden.
- Keyframe 2–3: Elements stay hidden.
- Move these keyframes on the timeline to set exactly when hiding occurs.
You can further tune the behavior by editing the Easing curve to define how motion between frames is interpolated — useful if you sequence Hide with other transitions.
Practical example
Consider an animation explaining an allosteric mechanism. Initially, you might want to show the whole protein, then zoom in and use Hide to remove structural elements that aren’t directly involved. This reduces visual noise and helps viewers focus on the relevant conformational changes. You can even choreograph multiple Hide instances to progressively remove pieces over time — like peeling away layers of the structure.
If you’re coming from earlier versions of SAMSON and remember the old Animation menu: note that it’s been replaced with the Animation panel inside the Animator interface. You can access it anytime through Ctrl + 7 or Cmd + 7.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it at https://www.samson-connect.net.