Organizing molecular structures spatially is a routine yet critical part of molecular modeling. Whether you’re preparing systems for simulations, illustrating interactions between molecules, or assembling complex biomolecular environments, correctly aligning and distributing molecules can prevent downstream errors and enhance clarity in visualizations.
Manually performing these spatial transformations often slows down workflows and introduces inconsistencies. Fortunately, SAMSON offers built-in tools for aligning and distributing atomic structures, meshes, and lights, which can significantly speed up the process. In this post, we’ll show how these features work and how you can use them efficiently.
Where to Find the Commands
The commands for aligning and distributing structures are located in the top menu bar:
- Edit > Align – for aligning structures with respect to global axes and planes.
- Edit > Distribute – for evenly spacing objects in the scene.
Aligning Structures Using the Context Menu
Right-clicking on a selected structure opens up a context menu. Under the Move selection submenu, you have fine control over alignment options relative to the global reference frame (XYZ axes and XY/XZ/YZ planes):
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, YZ, or XZ plane
This is particularly useful when importing structures from different sources or performing comparative structural analysis.
Using the Compass Widget
Another method involves the compass widget, a quick alignment tool embedded in the viewport. Right-clicking on it provides access to relevant alignment actions. This is a great option when you prefer not to navigate menus and would rather align objects interactively.
Why It Matters
Here’s how alignment and distribution can help in everyday molecular modeling tasks:
- Simulation setup: Ensure molecules are oriented correctly with respect to the simulation box or field conditions.
- Model building: Assemble complexes or periodic systems more systematically.
- Visualization: Create cleaner, more understandable graphics by avoiding randomized orientations.
- Teaching and presentations: Use consistent layouts to better communicate structural features.
The ability to visually and precisely position structures—without writing scripts or manually nudging atoms—is especially valuable for researchers who often switch between modeling and visualization tasks.
To dive deeper into how these tools integrate with SAMSON’s broader editing functionality, you can explore the full documentation page: https://documentation.samson-connect.net/users/latest/moving-objects/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.