When working with complex molecular systems, positioning multiple components accurately can become a real challenge. Whether you’re preparing simulations, building assemblies, or simply organizing structures for a better visual understanding, having intuitive tools for alignment makes all the difference.
This post explores how to align and distribute objects in SAMSON, the integrative platform for molecular design. From simple centering of molecules to structured alignment along axes and planes, SAMSON’s alignment tools are invaluable for efficient molecular modeling workflows.
Why alignment matters 🧩
In molecular modeling, precise spatial relationships affect properties, function, and interactions. You may want to:
- Align fragments before docking.
- Create arrays of molecules or nanoparticles.
- Prepare clean input files for simulations.
- Compare conformations side-by-side.
Global reference frame alignment
SAMSON allows you to align atomic structures with respect to the global XYZ frame. To do this:
- Right-click a structure in the Document View or directly in the viewport.
- Choose Move selection from the context menu.
- Select alignment options like:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, XZ, or YZ planes
This gives you quick and reproducible spatial arrangements across different molecules or fragments.
Align & distribute panels
You can also access structure organization features from the top menu under Edit > Align and Edit > Distribute. These allow you to:
- Align selected components at their centers along specific directions.
- Evenly distribute objects along a chosen axis or plane.
These tools help maintain symmetry and structure in molecular layouts, especially useful for materials science and supramolecular chemistry models.
The Compass widget approach
Add another layer of flexibility with the Compass widget. By right-clicking on it, you access actions to align the selection relative to axes or planes, offering another way to control spatial orientation.
Use cases and time-saving tips
- Protein assembly modeling: Distribute subunits along an axis with fixed separation.
- Nano-surface functionalization: Align ligands to match surface vectors.
- Molecular animation: Set initial positions to create smoother transitions.
Need a reference? Turn on the grid from the bottom of the viewport to visualize the XY plane at Z=0—helpful for understanding 3D transformations.
Try it yourself
Explore these tools with your own molecular data. Try combining alignment and distribution to dynamically structure complex assemblies.
Want to go further? Read the full documentation on Moving Objects in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.