Precise orientation of molecular models is essential in many modeling workflows, from preparing simulations and comparing molecular structures to generating reproducible visualizations. Yet, achieving consistent alignment can be tedious, especially when done manually.
If you’re working with molecular structures, meshes, or lights in SAMSON, aligning them within a well-defined global frame can help structure your workspace and save time during model setup and analysis. The good news? SAMSON makes this process intuitive through its built-in alignment tools.
What is the Global Reference Frame?
SAMSON uses a fixed reference system called the global reference frame, defined by X, Y, and Z axes and planes (XY, XZ, YZ). Aligning objects in this standard frame makes spatial relationships easy to interpret and ensures consistency across multiple sessions and models.
How to Align a Structure in the Global Frame
Follow these steps to align any atomic structure in the global reference frame:
- Right-click on the structure you want to align, or click on the current selection in the Document view.
- In the context menu, go to Move selection and choose your desired alignment option:
- Center on the origin
- Align with X / Y / Z axis
- Align with XY / XZ / YZ plane
This approach offers quick control over how your structures are oriented. For example, centering a molecular assembly at the origin and aligning it along an axis can help when comparing conformations or visualizing inter-molecular contacts.
Visual Aid: Use the Grid
To make alignment more intuitive, enable the grid in the Viewport using the bottom menu. The grid provides a visual representation of the XY plane (Z=0), helping you verify whether your objects are centered and leveled as intended.
Tips for a Smoother Workflow
- Combine with snapping: After aligning, use positioning tools like the Global Move Editor with snapping to fine-tune positions while maintaining symmetrical arrangements.
- Use compass actions: Right-click on the compass widget in the Viewport for additional alignment commands via SAMSON’s Compass interface.
These tools are especially useful when organizing multiple substructures, setting up assemblies for simulation, or preparing publication-quality renderings.
Aligned structures not only look cleaner, but also help avoid human errors when interpreting geometric data or applying symmetric transformations. Whether you’re modeling a ligand binding to a symmetric receptor or assembling nanoparticles, consistent orientation is critical.
To explore further use cases and learn how SAMSON handles object rotation and translation, visit the official documentation: https://documentation.samson-connect.net/users/latest/moving-objects/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.