You’ve arranged a molecular scene, added motion, and found a useful camera angle. Then you scrub to another frame—or export the movie—and the view has shifted. It’s a frustrating problem because the molecular motion may be correct while the story becomes hard to follow.
The key is to treat camera position, molecular position, and visibility as parts of the presentation timeline. In SAMSON, animations are organized as tracks in the Animator. Some animations change molecules; others change the camera or control how nodes appear. Planning those tracks together helps make a presentation more predictable when you edit, preview, and export it.
Start with a presentation and its timeline
Add a presentation through Visualization > Add > Presentation, or open the Animator and add animations there. A new presentation starts with an empty track view and a default duration of 180 frames. Double-click a presentation in the Document view to edit it in the Animator. Each animation has a track, and keyframes mark events or transitions on that track.
Think of the track view as a timeline for the scene, not just for the molecules. A docking animation, a camera move, and an appearance effect can all contribute to what the viewer sees at a given frame. You can preview a frame using the Animator controls or by selecting it directly in the track view.
Give the camera a defined job
Camera position can change while you work with a document or switch between presentation frames. If you don’t specify the camera state, a view that looked right during editing may not be the view you intended elsewhere in the presentation.
For a section that should remain still, add a Hold camera animation to define a static view. When you want the viewpoint to change, use an animation such as Move camera, Orbit camera, or Zoom camera. Camera animations can have controllers in the viewport, where you can adjust positions and orientations. If the controllers aren’t visible, zoom out in the viewport. While editing camera positions, thumbnails can show the current and neighboring keyframes, helping you compare shots.
A practical rule: decide where the camera should be at each important point in the story. Use an intentional camera move when the view should change; use Hold camera when it should not. This makes the camera’s role clearer and makes it easier to spot gaps while previewing.
Keep molecular motion and visibility deliberate
Motion animations include Assemble, Dock, Move atoms, and Play path. If you use motion animations, the documentation recommends considering Hold atoms at frames where no other motion animation is used. This can help keep structural nodes in their intended positions as you work with the document or change frames.
The same planning idea applies to visibility. Appear and Disappear create gradual changes, while Show and Hide change visibility at a frame. If nodes should remain consistently shown or hidden through parts of a presentation, explicitly set their state where needed. Visibility and transparency can also change during editing or when switching frames, so previewing the timeline is worthwhile.
Check order, then preview
Animations are applied in their order in the presentation. If multiple camera animations occur at the same frame, they are applied consecutively, and the camera state corresponds to the last one applied at that frame. You can change animation order by dragging items in the Document view. If a frame behaves unexpectedly, check both the keyframe timing and the order of the animations.
Scrub through the beginning, transitions, and end of the presentation before exporting. Look for sudden camera changes, unclear visibility, or molecular motion that isn’t held where expected. The Animator’s play controls also let you test the presentation as a sequence rather than judging each frame in isolation.
Export when the sequence is ready
Use Save movie in the Animator to export a presentation. The Save as dialog offers mp4, gif, and webm formats. The final result can depend on the global presentation options, which are available through the settings button in the Animator or under Interface > Preferences > Rendering > Presentations. Animation controllers are hidden during playback and export by default; this can be changed in presentation preferences.
A little timeline planning can prevent a common presentation problem: a scene that is scientifically sound but visually difficult to follow. Define the camera, molecular motion, and visibility at the points where the story changes, then preview before exporting.
Learn more in the SAMSON documentation on presenting and animating.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.