When designing complex molecular systems, positioning fragments in three dimensions can be both critical and challenging. Whether you’re assembling ligands, placing functionalized rings, or orienting biomolecular components for docking simulations or visualization, precise and flexible control over fragment orientation can save a lot of time.
SAMSON, the integrated molecular design platform, offers several practical tools to orient molecular fragments easily and effectively during building or editing. If you’ve ever struggled to rotate a methyl group into the right angle or align an aromatic ring across a bond axis, this guide is for you.
Choosing How to Move
Once a fragment is part of your system—either added from the Asset Browser or constructed manually—you may want to change its orientation. SAMSON offers a few different Move editors for this purpose:
- Local Move Editor (M): For rotating around a selected pivot, such as a specific atom or bond.
- Global Move Editor (K): For rotating and translating entire fragments based on a set origin and axes.
After selecting a fragment, press M to enable the Local Move Editor. The interface displays a controller sphere over the pivot point, which you can adjust. Zoom in and click on any atom in your selected fragment to make it the rotation center. Then use the gizmo to rotate the structure freely or around principal axes.
Rotating Around Bonds
Want to rotate a connected fragment around a given bond? Just click on the bond directly with the Local Move Editor active. The editor will automatically identify the connected fragment on one side of the bond and apply the rotation tools specifically to it. This allows you to perform quick conformational searches or generate new poses without affecting the rest of your model.
Snapping for Precision
If you’re positioning multiple fragments symmetrically, enable rotational snapping to rotate by fixed angles. This is especially useful for generating periodic units or symmetrical assemblies such as supramolecular cages.
The Global Move Editor (K) can also be used when you want to distribute copies of a molecule uniformly around a rotation axis. Define the pivot, enable snapping, and rotate each copy in increments (e.g., 90° or 120°).
Using these editors thoughtfully gives you fine control over how your fragments interact and helps in producing meaningful structural hypotheses.
Final Thoughts
Getting fragments into just the right orientation is a common task in molecular model building. SAMSON’s visual editors allow you to manipulate parts of your system interactively and intuitively. Whether you’re adjusting torsions or arranging binding modes, learning how to use the Local and Global move editors effectively is a valuable addition to any modeler’s toolkit.
To learn more and explore additional move editors and options, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/building-molecules/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.