One of the most common questions from molecular modelers preparing visual presentations or simulations is: How do I keep track of where atoms move during an animation? Whether you’re demonstrating a molecular docking sequence, a structural assembly, or the results of a dynamics simulation, it’s often crucial to record and visualize the paths atoms follow throughout your animation.
If you’re using SAMSON, the integrative platform for molecular design, there’s a simple but powerful way to do exactly that: the Record path animation effect. Here’s how it works and why you might find it useful in your next molecular animation.
Why record atomic paths?
Imagine you’ve just created an animation where a ligand travels through a protein tunnel and binds to the active site. The animation looks great, but now you want to emphasize how the ligand navigated that complex landscape. This is where the Record path animation comes in. It records a trajectory path followed by selected atoms and creates a visual trail summarizing their motion throughout the animation.
How to add the Record path animation
To start recording, double-click the Record path effect in the Animation panel. A keyframe will be added at the current timeline position in the Animator. You can move the keyframe to align with the portion of your animation where motion occurs.
Here’s the trick: SAMSON executes animations from top to bottom. That means the Record path effect should be placed after other animations modifying atomic positions—such as Assemble, Dock, Simulate, or Move atoms. Make sure you set the order correctly to get accurate trajectory data.
Visual feedback during recording
While recording, you get immediate visual feedback:
- Green track segments: indicate successful recording of atomic positions at a specific frame.
- Red track segments: indicate positions are either not yet recorded or no longer valid.
This feedback is especially helpful when debugging a complex animation sequence. Here’s what it might look like:
Once the path is recorded…
After playing through your animation and once the Record path is fully green, it’s time to extract the trajectory as a Path node into your document. You can do this in two ways:
- In the Inspector of the animation, click Create path.
- Or, right-click the Record path in the Animator and select Create path.
Tips for smoother workflows
If you’re still editing your animation or want to optimize performance, you can disable the recording temporarily. You’ll find the Enable recording option in the Inspector or by right-clicking the Record path in the Animator. When disabled, the controllers will appear darkened, indicating that recording is paused.
This small adjustment can significantly speed up editing, especially with complex structures and long animations.
Final thoughts
Adding this simple effect not only deepens your molecular animations but also provides a visual summary of motion that can be used in analysis, publications, or visual storytelling. Whether illustrating a ligand’s diffusion path or tracking structural reconfiguration, the Record path animation becomes a valuable part of your toolkit.
Learn more about the Record path animation in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.