A molecular animation can look correct while you are editing it, then feel inconsistent when you scrub the timeline or export the movie. The camera may no longer point where you expect, a structure may appear or disappear at the wrong moment, or moving atoms may not stay in the intended positions. These problems often come down to one issue: the presentation does not explicitly define enough of the scene’s state at key frames.
In SAMSON, a presentation combines animation nodes, and each animation appears as a track in the Animator. Some animations have keyframes that mark when an action begins and ends; others set states at particular frames. Thinking of the presentation as a sequence of scene changes—not just a collection of effects—makes it easier to build and troubleshoot.
Start with a prepared scene
Before adding motion, decide what the audience should see. Apply the needed visual models, choose visibility and color schemes, and set the viewport style. The Visualizing and Colorizing guides cover those setup steps. If the real-time viewport needs lighting, fog, clipping, shadows, or silhouettes, adjust Rendering effects before building the animation.
Then create a presentation with Visualization > Add > Presentation, or open the Animator and add animations from its Animation panel. Double-click a presentation in the Document view to edit it in the Animator. The Track view is where you can inspect timing, select frames, and preview how the scene changes.
Make motion states explicit
For molecular motion, use the animation that matches the task: for example, Assemble, Dock, Play path, or Move atoms. If you use motion animations, the documentation recommends considering Hold atoms at frames where no other motion animation applies to the structural nodes. This can help preserve intended positions as you work in the document or switch between presentation frames.
The same principle applies to the camera. Camera position can change while you work with a document, so a view that looks right during editing may not be reliably defined throughout the presentation. Use a camera animation at the relevant frames; when you want a static view rather than a camera move, Hold camera can define that view.
Camera controllers appear in the viewport for supported animations. If they are hard to find, zoom out; you can also show or hide controllers by checking the animation in the Document view or using its context menu. When editing camera positions, thumbnails for the current and neighboring keyframes can help you spot a framing change before it becomes an abrupt cut.
Plan visibility as part of the story
Use Appear and Disappear for progressive transparency changes, or Show and Hide to change visibility at a frame. To avoid unexpected visibility when moving between frames, specify which nodes should be shown or hidden at frames where no other entrance, exit, or highlighting effect sets their state. This is a useful safeguard, not a requirement for every presentation.
Check timing and order before exporting
Preview the presentation by moving through frames in the Track view, not only by pressing Play. Check the start, end, and transition frames: these are where camera changes, visibility effects, and molecular motion can overlap. Animations are applied according to their order in the presentation. If multiple camera animations occur at the same frame, they are applied consecutively, and the last one determines the resulting camera state. Reorder animations by dragging them in the Document view when needed.
Once the sequence is stable, use Save movie in the Animator and choose a supported format such as MP4, GIF, or WebM. Export behavior can depend on the global Presentation options, which are available through the Animator settings button or Interface > Preferences > Rendering > Presentations. If the exported result differs from the preview, check those options and confirm that the relevant camera, motion, and visibility states are defined across the frames.
For more details on presentations, animation types, and export settings, see the SAMSON presenting and animating documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.