Turning Molecular Models into Simple Movies with SAMSON’s Animator

Creating scientific presentations using static images can make it hard to clearly communicate complex molecular processes such as docking, folding, or dynamic interactions. For molecular modelers, visualizing a sequence of changes in molecular configurations is not just attractive—it’s often essential. This is where SAMSON’s Animator comes in.

SAMSON provides a built-in Animator tool to create molecular presentations and movies that clearly demonstrate molecular interactions, structural assemblies, or camera motions. Whether you’re preparing a talk, a poster, or simply trying to understand a phenomenon better, turning your molecular scenes into animated stories can help.

What Is a Presentation in SAMSON?

A Presentation is a special kind of node in a SAMSON document. It contains animations applied to molecular or visual elements, cameras, or even slide-like backgrounds. Those animations can be chained and timed to form an interactive or self-playing movie exported in common formats such as MP4, GIF, or WebM.

Each animation is added as a track in the Animator, which has a timeline-based editing system where you can:

  • Play and stop the animation
  • Move or adjust timing of keyframes
  • Add or reorder animations using drag-and-drop

The Animator with a presentation opened in it

A Quick Workflow Example

Let’s say you want to create a simple animation of a protein structure appearing while the camera orbits around it. Here’s how you would do it:

  1. Open or fetch a molecular structure in SAMSON. For instance, using Home > Fetch to load 1AF6 from the PDB.
  2. Apply a visual model such as Ribbons to the structure.
  3. Add a presentation via Visualization > Add > Presentation. The Animator will open automatically.
  4. Select the Ribbons model, then double-click on the Appear animation in the Animation panel (right side).
  5. Position the camera, then double-click the Orbit camera animation to add camera movement.

You can click play to preview your animation. Adjust timing by dragging keyframes in the timeline view. You can also fine-tune the animation using the Inspector panel.

Fine Camera Control with Thumbnails

While editing animations that involve camera movement (such as Move camera), thumbnails appear at the bottom of the 3D view to help you see previous and next positions. This feature is especially helpful when adjusting transitions to avoid jumps or unnecessary shifts in framing.

Camera snapshots tutorial

Exporting Your Work

Once satisfied, you can export your animation as a movie. Just click the Save movie button in the Animator and choose your format. Final movies can be shared in presentations, embedded in papers, or used in class to explain a concept visually.

Useful Tips

  • You can pause and resume presentations using Space.
  • Using the Hold camera animation ensures static camera views remain consistent.
  • Global preferences let you control default backgrounds, watermarking, and rendering options.

Collaboration and Sharing

Presentations can be saved within a SAMSON document and shared with collaborators or the community through SAMSON Connect – Documents. Contributors can download, play, and even extend your animations on their systems.

To dive deeper into creating and editing presentations, visit the full presentation documentation page: https://documentation.samson-connect.net/users/latest/presenting/

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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