If you’ve ever prepared molecular animations for presentations, publications, or teaching, you’ve probably faced a frustrating challenge: how do you control exactly when a molecule (or part of it) appears in an animation? Whether you’re explaining a reaction mechanism or visualizing macromolecular interactions, showing molecules at the right time is key to clarity. That’s where the Show animation in SAMSON can help.
The Show animation effect allows specific elements of your molecular model (called nodes) to suddenly appear at a precise moment, remain visible until the end of the animation, and be completely hidden before their entrance. This distinct behavior makes it an effective tool for telling molecular stories step-by-step, especially important when clarity and timing are essential.
One Animation Instead of Two
The Show animation combines what would otherwise require two separate effects—Hidden followed by Shown. This simplicity reduces clutter in your animation panel and keeps your workflow more efficient.
How It Works
The Show animation uses three keyframes:
- Keyframe 1 to 2: The selected nodes are hidden.
- Keyframe 2: The nodes instantly appear.
- Keyframe 2 to 3: The nodes remain visible.
This creates a clean visual entrance of specific parts of your model—especially useful for focus points like a ligand docking site, catalytic residues, or newly formed molecular assemblies.
To use this function:
- Select the nodes you want to appear.
- Go to the Animation panel under the Animator.
- Double-click on the Show animation.
- Adjust keyframe positions as needed to control the timing of the appearance.
Timing and Presentation Control
You can always move the keyframes around, allowing fine-tuned control over animation timing—something particularly valuable during educational presentations or product demos. For smoother transitions or stylistic effects, customize how parameters are interpolated between frames by adjusting the easing curve.
Why Use Show Instead of Transparency?
It’s important to note that Show relies on visibility, not transparency. Transparency effects can become confusing when layered molecular structures overlap—leading to unclear visuals. The Show animation avoids this problem by hiding the nodes entirely before they appear.
Example in Action
Here’s an example GIF extracted from SAMSON’s documentation. Notice how molecules appear suddenly and stay visible, producing a cleaner and more focused animation:
When to Use It
- Introducing ligands or cofactors in an enzymatic mechanism
- Step-by-step assembly or disassembly of macromolecular complexes
- Highlighting structural differences in mutant vs. wild-type proteins
- Adding secondary structure elements one at a time during a lecture
If you’re aiming to make your molecular animations clearer and more engaging, the Show animation provides a focused and non-ambiguous way to control the visibility of molecular components over time.
Learn more about the Show animation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.