When preparing a molecular animation, it’s easy to face one frustrating issue: unnatural atomic jumps from one frame to the next. Whether you’re presenting a conformation transition, simulating a nanotube breathing cycle, or demonstrating ring flipping, discontinuous movement can make even scientifically accurate animations look strange to viewers.
A helpful solution to this issue in SAMSON is using keyframes with the Move atoms animation. This feature allows you to create smooth transitions by interpolating atom positions between defined frames. Instead of snapping atoms from one location to another, you guide their path—just like animators do in movies.
What are keyframes?
Keyframes act like waypoints in time. You define a structure’s configuration (i.e., the positions of atoms) at certain frames, and SAMSON automatically interpolates between them. This creates the illusion of freely moving atoms with minimal effort.
Here’s how it works:
- Position the atoms how you want them to appear at the start.
- Select them, and double-click the Move atoms animation in the Animation panel.
- This adds the first keyframe at the current frame.
- Advance the animation timeline, reposition the atoms (using transformation tools or other editors), and a second keyframe is automatically created.
Fine-tuning motion with easing curves
Once you define keyframes, the animation’s smoothness can be further refined. The Inspector panel lets you change the interpolation mode via easing curves. You can choose between linear interpolation (constant speed), ease-in (slow start), ease-out (slow end), or ease-in-out transitions. This is particularly useful for molecule assembly demos or slow folding sequences.
Mixing animation controllers and manual editing
Sometimes, finer control is needed than what the default animation controllers allow. You can:
- Hide the Move atoms controllers from the Document View.
- Switch to tools like the Move editors or Twister editor to manually apply transformations.
- Place a new keyframe whenever the new configuration is ready.
- Switch back to the Select editor once editing is done.
Editable and removable
Animations should not be final until you are satisfied. SAMSON allows moving or removing keyframes easily. Right-click on any keyframe in the Track view and select Remove keyframe to fix mistakes or restructure your animation.
Applications in molecular modeling
Here are a few cases where keyframed animations provide meaningful visualizations:
- Transition between conformers or docking poses.
- Simulating breathing or vibration in molecular assemblies.
- Interpolating molecular mechanics simulations.
- Creating visually continuous reaction steps or folding demos.
By mastering keyframes, not only do your molecular animations look more natural, but they also become more communicative, especially for audiences not familiar with abrupt atomic movements.
To explore more capabilities and practical examples such as nanotube animations using keyframes, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/move-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.