Creating compelling molecular animations can be one of the most time-consuming tasks for researchers preparing publications, presentations, or outreach material. While modern tools offer advanced visualization options, they often lack intuitive ways to manage complex animation timelines, leading to frustration and lost time.
If you’re a molecular modeler searching for a visual timeline editor where you can precisely control when and how animations occur — such as atoms assembling, rotating, appearing or disappearing — the Track view in the Animator panel of SAMSON may be exactly what you’ve been looking for.
Why It Matters
Animations in molecular modeling aren’t just eye candy. They’re powerful tools for communicating mechanisms, transitions, and spatial relationships—processes that are often hard to convey through static images. However, managing these animations can get complex quickly, especially if you have multiple coordinated movements involving atoms and cameras over time.
Introducing Track View
In SAMSON, the Track view offers a timeline-based interface to graphically manage animations. It’s located in the central area of the Animator panel and operates similarly to video editing software timelines — a familiar concept to many users.
Each animation track corresponds to a specific animated node or event and includes one or more keyframes, which are moments where something specific happens—e.g., a molecule appears, a camera changes angle, or atoms start to move.
Key Features
- Multi-track support: work with multiple animations in parallel (camera motion, atom transformations, labels, etc.).
- Color-coded tracks: quickly identify different animation types like movement, camera, entrance/exit effects, etc.
- Time navigation: scrub through your animation or jump to important frames.
- Drag-and-drop: reposition keyframes or re-order animations easily.
- Preview integration: real-time feedback as you edit frames allows for intuitive alignment of events.
Track View in Action
Let’s say you want to zoom into a binding pocket while the molecule slowly assembles. In SAMSON’s Track view:
- Drag a Move camera animation to your desired timeframe.
- Add an Assemble motion animation for the molecule.
- Choose an Appear effect to fade the model in gradually.
- Adjust their keyframe positions to align visually and temporally.
The result is an animation that builds your molecule while positioning the camera smoothly, fully customizable from a visual timeline. This greatly reduces the guesswork and iteration needed when trying to achieve professional-looking animations.
Best Practices
- Add a Hold camera effect if you don’t want camera movement at a specific frame. This ensures the viewport stays consistent.
- Use pulse or highlight effects to draw attention to key molecular features.
- Keep track of visibility by explicitly setting Show or Hide animations to avoid unexpected behavior during playback.
Conclusion
The Track view in SAMSON provides a precise and intuitive way to build and coordinate animations across complex molecular structures. Whether you’re trying to show ligand binding, conformational changes, or a molecular system unfolding over time, this tool lets you align everything clearly and visually.
To learn more about how to use the Animator and Track view in SAMSON, visit the 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.