Making Molecules Fade In: The ‘Appear’ Animation in SAMSON

When preparing scientific presentations or educational videos, molecular modelers often face a challenge: how to visually introduce complex molecular structures in a way that feels fluid and intuitive to viewers. A sudden jump from an empty scene to a fully detailed molecule can be jarring and distract from the message being delivered. To address this, SAMSON provides an elegant solution: the Appear animation.

Rather than displaying molecules instantly, the Appear animation lets your selected molecular nodes fade in smoothly, creating a more polished and professional experience. This is especially effective when you’re constructing videos to highlight molecular mechanisms, dynamic processes, or simply introducing elements step by step in a visual narrative.

What It Does

The Appear animation progressively decreases the transparency of compatible nodes, transitioning them from invisible to fully visible. These nodes include:

By applying the Appear effect to these nodes, you can ensure they fade into view gradually, rather than pop into existence.

How It Works

The Appear animation is built around four keyframes:

  • Keyframe 1 → Keyframe 2: Nodes stay fully transparent.
  • Keyframe 2 → Keyframe 3: Nodes become less transparent, gradually appearing.
  • Keyframe 3 → Keyframe 4: Nodes are fully visible (no transparency).

You can reposition keyframes along the animation timeline to control how long each phase lasts. For example, keeping the fade-in between frames short will make the appearance feel quick, whereas stretching it will create a slower, more cinematic reveal.

Example: the Appear animation

Tips for Effective Use

Here are a few suggestions to get the most out of the Appear animation:

  • Apply it to the structural models rather than individual atoms or bonds—only the full model has a transparency property.
  • Combine with the Disappear animation to create complete transitions in and out.
  • Use the easing curve editor to fine-tune how the transparency changes for smoother results.
  • Leverage this animation to build layered stories: start with labels or outlines, and then fade in full molecular detail.

Adding the Animation

Here’s a step-by-step to apply the Appear animation:

  1. Select the nodes you want to animate.
  2. Open the Animation panel in the Animator.
  3. Double-click on the “Appear” animation effect.
  4. Adjust the keyframes to match your presentation timing.

Using this technique, you can lead your viewers into complex molecular scenes instead of dropping them in all at once.

To learn more, visit the official SAMSON documentation on the Appear animation: https://documentation.samson-connect.net/users/latest/animations/appear/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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