Tired of Static Molecules? How to Bring Your Molecular Systems to Life for Presentations and Publications

Creating compelling molecular animations can be time-consuming — especially when shifting between research tools and video editing software. Molecular modelers often face the challenge of clearly explaining dynamic phenomena such as docking, conformational changes, or assembly mechanisms. Static images often fall short.

Fortunately, SAMSON offers a wide set of built-in animation tools tailored to molecular systems. These animations can help you illustrate complex processes like docking or conformational shifts, generate publications-ready videos, or create visual content for teaching without relying on external tools.

Let’s walk through how you can start making animations in SAMSON using the built-in Animator panel.

The Animator and Animation Panel

SAMSON no longer uses the old Animation menu; everything is now centralized in the dedicated Animator panel. Through this panel, you can sequence and control a large number of animations that act on cameras, atoms, molecular models, meshes, and more.

You can organize your animation sequences from one interface and preview how different actions (like atom movement or camera orbit) appear in your scene. The Animator also allows you to control durations, transitions, and visual effects — which simplifies the creation of step-by-step molecular movies.

Categories of Animations

Animations are divided into several functional groups:

  • Motion animations: like Dock, Assemble, and Move atoms, useful for showing chemical interactions or processes.
  • Camera animations: including Orbit camera and Play path, help guide viewers’ attention.
  • Entrance/Exit effects: effects such as Appear, Disappear, Reveal atoms, or Hide enable clarity in sequential storytelling.
  • Highlighting effects: like Pulse, to emphasize molecular features or active sites.
  • Other animations: including Pause, Stop, and Set background for presentation control.

Practical Use Case: Showing Docking with Motion & Camera

Suppose you’re presenting a protein-ligand docking scenario. You can:

  1. Use Dock to animate the ligand binding to the active site.
  2. Combine with Orbit camera to rotate around the protein and provide audience perspective.
  3. Add a Pulse animation at the binding site for emphasis.
  4. Insert a Pause to stop the motion momentarily and explain.

The result is a reusable, narratable animation that visually illustrates a molecular interaction — without the need to exit SAMSON or post-process footage.

Comprehensive Animation Library

SAMSON includes over 30 individual animations, each with a specific role. These range from simple actions like Show and Pulse, to complex guided motions like Play path or Record path.

You can browse the complete list here and mix-and-match these actions to fit your storytelling needs — from basic entrance effects to full molecular simulations.

Video Tutorial

If you prefer a visual overview, check out the video tutorial: How to create molecular animations in SAMSON.

This short guide introduces how to use the various animation tools and panels, although note that it shows the earlier Animation menu, which has since been replaced by the Animator.

Conclusion

Animations in SAMSON offer an intuitive way to clearly convey atomic-level events, making your research more accessible and your presentations more informative. From basic effects to complex assemblies and movements, the Animator helps you build visual narratives directly within your modeling environment.

For the full documentation, visit the Animations page on the SAMSON documentation site.

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

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