When building molecular systems in SAMSON, many molecular modelers encounter the same challenge: how to precisely control the positioning and orientation of fragments when assembling complex molecules. Whether you’re bonding ligands to a central atom or assembling repeat units in a polymer, precise geometric control is crucial—for both visual clarity and accurate simulation.
In this post, we explore how SAMSON helps you orient molecular fragments effectively using interactive tools. SAMSON’s move editors offer a user-friendly and responsive way to rotate, position, and align fragments—even after adding them to a structure. This can greatly improve your modeling workflow, especially when preparing systems for simulations or presentations.
Overview: Why Orientation Matters
Incorrect fragment orientation can lead to overlapping atoms, distorted geometries, or unrealistic bond angles, which in turn affect energy minimization and simulation results. Adjusting orientations manually in some software can be time-consuming or imprecise—but SAMSON provides specific tools for the job.
Using the Local Move Editor
Once you’ve added a fragment, it is automatically selected. If not, you can select it easily in either the Document view or Viewport.
To orient the fragment, just activate the Local Move Editor with the shortcut M. With this editor, you get rotation and translation controls directly on the selected fragment.
To define a custom pivot point for rotation (e.g., a central atom or a specific bond):
- Zoom in so the atom you want is clearly visible and not hidden by the rotation sphere.
- Click the desired atom to set it as the rotation pivot.
- Drag the rotation handles or click and drag the sphere to rotate freely.
This is useful for fine-tuning ring stacking, side chain positioning, or orienting ligands in a binding pocket.
Rotate Around a Bond
Need to rotate a part of a molecule around a specific bond? SAMSON simplifies this too. With the Local Move Editor active, just click the bond you want to rotate around. SAMSON automatically selects the bonded fragment and enables rotational controls specific to that axis.
Using the Global Move Editor
If you’re assembling symmetric structures or manipulating multiple fragments simultaneously, try the Global Move Editor (K). It works similarly to the local version but operates on a global coordinate system, making tasks like radial arrangements or tiling structures more intuitive.
For example, you can construct a central core and place multiple identical units around it with consistent angles by combining copy-paste functionality with rotational snapping.
Tips and Best Practices
- Always set your pivot point intentionally to avoid unintended rotations.
- Use
Shift + right-clickto rotate fragments before placement when building. - Combine with interactive minimization (shortcut
Z) to see how structures adapt dynamically when you move fragments.
Mastering these move tools will help ensure that your structures are not just chemically accurate but also visually intuitive and ready for the next steps in your modeling pipeline.
You can learn more about fragment orientation and movement tools in the official documentation here: https://documentation.samson-connect.net/users/latest/building-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.