When building complex molecular models, one of the recurring challenges is aligning functional groups or fragments precisely and efficiently. Incorrect orientation can result in steric clashes, unrealistic geometries, or simply more work adjusting everything afterwards. If you’ve ever tried rotating pieces into place atom by atom, you know this can be frustrating and time-consuming.
SAMSON provides intuitive tools to tackle this problem by letting users orient molecular fragments precisely using interactive move editors. With just a few clicks, you can rotate parts of molecules around specific atoms or bonds, placing everything where it needs to be.
Using the Local Move Editor
To orient a fragment you’ve just added (or selected), activate the Local Move Editor using the shortcut M. This tool allows you to rotate and move selections in a physically intuitive way via a 3D controller overlaid in the viewport. Here’s how it works:
- Click on a fragment to select it
- Press M to activate the Local Move Editor
- Click on an atom to set it as the rotation pivot
- Use the on-screen controller to rotate or move the selection around this pivot
This tool is especially useful after adding a new group like an N-acetyl, where the automatic orientation might not be optimal. With snapping turned off, fine adjustments are straightforward.
Rotating Around Bonds
What if you want to rotate part of a molecule around a single bond, like an ethyl side chain? SAMSON makes this just as simple. With the Local Move Editor active, click directly on the bond. SAMSON will automatically identify the smaller connected fragment and allow you to rotate it in-place. No need to manually select atoms or guess the rotation axis.
Here’s a demonstration (note: opens in YouTube).
Using the Global Move Editor
Another feature useful for orienting fragments—especially entire molecules—is the Global Move Editor (shortcut: K). It works similarly to the Local Move Editor but changes the entire model at once. This is perfect when working with molecular assemblies, placing components symmetrically, or working with periodic structures.
You can even define snapping angles and set pivot atoms for rotation, making it easy to align molecules relative to one another—or to a reference coordinate system.
Tip: Hold Shift and right-click to rotate fragments before adding them to your structure. This is particularly useful when assembling repeating units like phenol in polymer chains.
Why It Matters
Whether you’re refining a ligand binding mode or connecting consistent fragments into a Macromolecule, fragment orientation can quickly impact the realism of your model. SAMSON reduces friction by letting you focus on the chemistry, not the geometry handles.
To dive deeper into fragment orientation and other molecular modeling workflows, check out the full Building Molecules documentation: https://documentation.samson-connect.net/users/latest/building-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.