Making Molecules Fade into View: A Simple Way to Enhance Molecular Presentations

When presenting molecular systems, clarity and focus are everything. But when everything appears on screen at once, it often becomes hard to direct attention where needed. This is especially important in educational videos, presentations, or when preparing materials for grant proposals. Researchers often struggle to highlight specific components of molecular models progressively in a clean, visually intuitive way.

That’s where the Appear animation in SAMSON comes in handy.

What Does the Appear Animation Do?

The Appear animation lets you make selected molecular components fade into view smoothly. Instead of a sudden jump from hidden to visible, nodes with a transparency attribute—like structural models, meshes, visual models, or labels—transition gradually from transparent to opaque.

This small effect can make a big difference in understanding. It subtly guides viewers’ attention and emphasizes flow in molecular processes like ligand binding, conformational changes, or structural comparisons.

What It Works On

To use the Appear animation, you must apply it to nodes that support transparency. These include:

Note that individual atoms or bonds themselves don’t have an opacity attribute but their container (the structural model) does. If you want an entire set of atoms to fade in, apply the effect at the structural model level—not at the atom or bond level.

Using the Appear Animation in SAMSON

  1. Select the nodes you’d like to gradually appear.
  2. In the Animation panel of the Animator, double-click the Appear effect.

The animation contains four keyframes:

  • Between keyframes 1 and 2: nodes are fully transparent.
  • Between keyframes 2 and 3: nodes fade in (transparency decreases).
  • Between keyframes 3 and 4: nodes are fully opaque.

You can drag keyframes to control how fast or slow the animation progresses. For instance, a longer delay between keyframes 2 and 3 makes the fade-in slower for dramatic effect.

Optional: Fine-Tune with Easing Curves

SAMSON allows you to adjust the interpolation of transparency over time using Easing curves. For example, you can apply a linear interpolation for steady change, or ease-in/out for smooth acceleration and deceleration.

Note on Interface

Some older tutorials still mention an “Animation” menu. Since that menu is no longer part of SAMSON, all animations are now accessed via the Animation panel, either through the GUI or using the shortcut Ctrl + 7 (or Cmd + 7 on Mac).

Example: the Appear animation

When Should You Use It?

Here are just a few useful scenarios for the Appear animation:

  • Explaining how a drug binds to a protein
  • Presenting alternative conformations
  • Demonstrating the step-by-step construction of a molecular complex
  • Highlighting specific functional domains in a biomolecule

Adding this subtle animation can make your presentations easier to follow and more effective at conveying complex ideas to any audience—not just specialists.

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

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

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