When preparing scientific presentations or educational videos using molecular models, one of the common challenges is selectively focusing the viewer’s attention on specific parts of a system. For molecular modelers and educators alike, this often means finding a way to temporarily hide parts of a complex structure without permanently altering the model—or confusing the audience with partial transparency or overly busy visualizations.
This is where the Hidden animation in SAMSON, the molecular design platform, comes in handy.
Why use the Hidden animation?
The Hidden animation allows users to make selected nodes in a molecular system disappear and reappear between two keyframes. Unlike changing transparency or using clipping planes, this simply hides the nodes completely, making the visualization cleaner and more direct for audiences who don’t need to see everything at once.
Importantly, this feature works using the visibility of nodes rather than their transparency—ensuring a hard cut visibility toggle that’s easier to interpret. This is especially useful during animations that demonstrate mechanisms or molecular interactions step-by-step.
Step-by-step: How to apply the Hidden animation
- First, identify and select the nodes you want to hide. These might be ligands, residues, membranes, or even entire subunits you want to temporarily remove from view.
- Open the Animator in SAMSON.
- In the Animation panel, double-click on the Hidden effect. This will automatically set the start keyframe at the current position in the timeline.
- Move ahead in the timeline and add or adjust the end keyframe to control when the nodes reappear (or remain hidden).
Tip: You can always reposition the keyframes to adjust the timing of the animation. This is helpful for synchronizing the hiding and showing of molecular components with other animated effects like rotations or zooms.
When should you use it?
Here are a few scenarios where the Hidden animation can enhance your presentation or molecular storytelling:
- Demonstrating ligand binding: start with only the binding pocket visible, then reveal the full receptor.
- Explaining enzyme mechanisms: hide less-relevant chains to focus on catalytic residues.
- Educational walkthroughs: progressively reveal subsystems to follow the workflow of a molecular process.
Visual Example
Below is a sample animation from SAMSON showcasing how “Shown” and “Hidden” combine to reveal and conceal groups of atoms in a protein structure:
Note: In some videos or older versions of SAMSON you might see references to an Animation menu. This has been replaced by the Animation panel within the Animator interface. You can access it via the Ctrl + 7 (or Cmd + 7 on macOS) shortcut.
Fine-tuning the feel
The Easing curve allows you to customize how the animation progresses over time. For instance, you can choose to make elements fade out quickly at first, then slowly disappear—or vice versa—giving you more control over the pacing and rhythm of your visual storytelling. Learn more about it in the easing curve documentation.
Animations like Hidden give you fine-grained control over your molecular models, allowing you to create clean, focused visual narratives for presentations or recordings.
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.