When preparing scientific animations of molecular systems, one common challenge is showing and hiding molecular components in a clear, meaningful way. For example, when describing a binding pocket or illustrating conformational changes during a simulation, you may want some atoms or groups to visually disappear from the scene to focus attention elsewhere. Doing this smoothly, without relying on ambiguous transparency or manual edits, can save time and improve clarity.
The Hide animation in SAMSON offers a simple solution to this. It lets you make specific nodes (e.g., atoms, molecules, groups) disappear at a given moment in your animation timeline by adjusting their visibility—not their transparency. This can be more intuitive to viewers, especially in presentations or publications, because the object is either present or not, with no semi-visible in-between.
How it works
Applying a Hide animation effect is straightforward. Once you’ve selected the nodes you want to hide, double-click the Hide effect in the Animation panel of the Animator. The animation consists of three keyframes:
- Between keyframes 1 and 2, the nodes remain visible.
- At keyframe 2, the nodes are hidden.
- From keyframe 2 to 3, the nodes remain hidden.
This design allows for precise timing—especially useful when synchronizing with narration or other visual elements.
Why not transparency?
In many molecular visualization tools, a common way to de-emphasize parts of a structure is to make them transparent. This can sometimes work, but it runs the risk of visual clutter. Transparency still shows the shape of the atoms, which can cause distraction or confusion, especially when building educational content or communicating to non-specialists. By cleanly removing a node from view, the Hide animation simplifies the scene.
Tips for using Hide effectively
- Use in combination with the Show or Appear animations for more dynamic sequences.
- Be mindful of the timing—move keyframes to match the narrative flow.
- Remember, the visibility change occurs at keyframe 2—this is where emphasis should shift.
Customize with Easing Curves
Though this animation changes visibility directly (not gradually), you can still fine-tune how the timing interacts with other animated elements by adjusting the Easing curve. Easing affects how animations accelerate or decelerate, which can subtly influence how natural your full sequence feels.
This visibility-based approach can simplify the way you tell molecular stories, cleanly separating different stages, sites, and components of a process or structure. Whether you’re teaching, writing a paper, or crafting a scientific movie, knowing how to effectively hide and reveal structure is an invaluable tool.
To dive deeper and see the full documentation on the Hide animation, including other related effects like Disappear and Flash, you can visit the official SAMSON page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.