Creating Molecular Animations Without Writing a Single Line of Code

Presenting complex molecular mechanisms to collaborators, students, or within publications often requires far more than static images. But creating dynamic, high-quality animations can be time-consuming, especially if it involves coding or video editing tools unfamiliar to most molecular modelers.

If you’ve ever delayed a presentation simply because animating your molecular model seemed too technical, SAMSON provides a no-code solution designed with you in mind.

What Can You Animate?

In SAMSON, you can animate both molecular structures and the camera itself. Whether you’re zooming into an active site, rotating around a docking event, or making a ligand appear at just the right moment—animations help explain your science more clearly.

Types of Animations

Animations in SAMSON are grouped into categories based on what they affect. Here’s a quick overview:

  • Motion animations: Movement of atoms or molecules (e.g., Assemble, Dock, Move atoms)
  • Camera animations: Movement of the viewer’s perspective (e.g., Orbit camera, Zoom, Play path)
  • Entrance/Exit effects: Visibility changes like Appear, Disappear, Hide, or Show
  • Highlighting animations: Draw attention with pulses or flashes
  • Other: Pause frames, background changes, and more

How It Works

Instead of relying on scripts or external visualization tools, SAMSON offers an Animation panel inside the Animator module. This replaces the older “Animation” menu and simplifies the animation workflow tremendously.

Here’s what you can do with just a few clicks in the Animator:

  • Drag and drop animation events onto a timeline
  • Preview animations instantly
  • Combine multiple object and camera events
  • Export your animation to create movies or screenshots

Use Case Example: Docking Animation

Imagine you’re modeling a protein-ligand interaction. To animate the ligand docking process, you can use:

  • Dock – brings the ligand into position
  • Rotate – orients the molecule over time
  • Orbit camera – shows the docking from different angles
  • Pulse – highlights the active site

Combined in a timeline, these events let you quickly build a visually compelling explanation of your mechanism.

Video Tutorial

To see a full animation workflow in action, the documentation provides a thorough tutorial: How to create molecular animations in SAMSON. Please note, the video refers to an older version (using the now-removed Animation menu), but the same functionality is available and improved in the Animation panel.

Animation Gallery

Here’s a sample screenshot of the Animation panel interface:

Animation Panel in SAMSON

And for those who want to explore all available animations, there’s a full alphabetical list available in the official documentation. From Appear to Zoom camera, there are more than 30 different animation types to use in sequence or combination.

If you’re interested in automating complex molecular presentations or explaining simulations with more clarity, the animation tools in SAMSON are worth exploring.

To discover the full list and purpose of each animation, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/

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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