Creating Molecular Animations and Presentations in SAMSON: A Practical Introduction

Animations are a powerful way for molecular scientists to communicate complex structures and phenomena clearly. Whether you’re teaching molecular docking, showcasing a simulation, or presenting a structural transformation, effective animations save time and help others understand your work faster. But for many modelers, creating animations feels like a separate skill—something that requires additional software, complicated workflows, or long render times.

SAMSON offers an integrated approach to building molecular animations and exporting them as movies, within the same environment you use for molecular modeling. This blog post introduces the Animator in SAMSON and demonstrates how to start building effective scientific visuals directly from your modeling work.

What is the Animator?

The Animator panel in SAMSON is a dedicated interface to assemble, manage, and play back molecular animations and presentations. It’s not just for flashy effects: it’s designed for practical storytelling—from docking simulations to structural breakdowns—all reproducible, trackable, and directly exportable as videos.

The Animator with an opened presentation

Three Key Areas of the Animator

  • Controls Section (top): manage playback behavior, define frame ranges, fine-tune presentation duration, and tailor global preferences.
  • Track View (center): visualize and modify the timeline of your animations—each with its own colored track and keyframes.
  • Animation Panel (right): browse and apply animations from six categories, including entrance and exit effects, camera paths, and molecular dynamics effects.

How to Start Your First Animation

Start by creating a new presentation via Visualization > Add > Presentation. This will open the Animator window. Then:

  1. Select a structure in the Document view.
  2. Double-click on an animation in the Animation Panel (e.g., “Orbit camera”).
  3. Use the track and timeline to move or adjust keyframes.
  4. Use camera controllers in the viewport to refine your view.

Adding the orbit camera animation

Tweaking Your Animation

The Animator supports thumbnails to help you frame your visual narrative as you position keyframes:

Advanced keyframe camera motions

You can fine-tune effects like timing curves (using easing functions), transparency level, and positional accuracy, by selecting animation nodes and editing their properties in the Inspector.

Making Things Disappear or Appear

One of the simplest and most powerful illustration techniques is revealing or concealing molecular elements progressively. Try it using the Appear and Disappear animations. For example, apply Disappear to the structural model to fade it out, while simultaneously applying Appear to a visual representation like Ribbons:

Adding the Disappear animation

Adding the Appear animation

Exporting Your Work

Once you’re satisfied with your animated sequence, click the Save movie button in the Animator toolbar. Choose your preferred format (MP4, GIF, WebM), and share your work—even embed it in presentations or papers.

Final Thoughts

For many scientists, showing is more efficient than describing. The animation tools built into SAMSON are not only accessible but designed to support scientific communication without the need to switch to other platforms.

To learn more about animation and presentation features in SAMSON, explore the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. Try it today at www.samson-connect.net.

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