Creating smooth molecular presentations with SAMSON’s Animator panel

Sharing scientific discoveries effectively often means going beyond static visuals. Molecular modelers today are increasingly asked to create engaging and clear presentations, whether for publications, teaching, or collaboration. One recurring challenge is: how to animate molecular scenes smoothly, without spending hours on complicated animation software.

SAMSON, the integrative platform for molecular design, addresses this with a dedicated Animator panel that simplifies the process of creating molecular animations. If you’ve tried to animate molecular structures before, you may have faced difficulties adjusting camera angles, introducing or removing structures gradually, or showing assemblies in action — all while trying to keep your audience focused.

Here’s a walkthrough of how SAMSON’s animation system helps solve that pain.

Animations tailored for molecular precision

The Animator panel in SAMSON gives users access to a wide range of animations. These are not generic video transitions — they’re specifically built for molecular modeling tasks. For example:

  • Appear and Disappear let you introduce or remove molecular structures gradually.
  • Dock and Undock show molecular assemblies coming together or moving apart.
  • Move atoms and Rotate are useful when highlighting conformational changes or interactions.
  • Highlighting animations like Pulse direct viewers’ attention to important regions.
  • Camera path animations (e.g. Orbit camera, Play path) enable smooth cinematic sweeps over molecular landscapes.

This targeted set of tools means you spend less time trying to “hack” a general-purpose animation system, and more time focusing on the science you want to communicate.

Organized for clarity

Animations in SAMSON are grouped into categories that reflect their function:

  • Motion animations: Show molecules assembling, docking, or disassembling.
  • Camera animations: Move the point of view smoothly around your model.
  • Entrance/exit effects: Introduce or remove models in eye-friendly ways (e.g. Appear, Disappear).
  • Highlighting effects: Where attention needs guidance.
  • Other animations: Including tools for changing slide backgrounds or pausing a presentation mid-flow.

This structure makes it easy to find the animation you’re looking for, even if you’re new to the platform.

From static scene to dynamic storytelling

Let’s say you want to demonstrate a ligand docking into a protein pocket. You might combine:

  • Dock to simulate the ligand approaching the pocket
  • Pulse to highlight key active site residues
  • Orbit camera to showcase the final configuration with a smooth camera path

All of that — without scripting or leaving the SAMSON environment.

Getting started

Watch the tutorial: How to create molecular animations in SAMSON. Note that the video mentions a now-deprecated Animation menu — all animations are currently accessible from the Animator panel.

Animation Panel in SAMSON

To explore the full list of animation options available in SAMSON and how to apply them, visit the Animations documentation page.

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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