Manipulating dihedral angles is a common task in molecular modeling, especially when preparing conformational ensembles, exploring molecular flexibility, or setting up simulations. For many scientists, this operation can be cumbersome and tedious in overly complex or rigid software interfaces.
In SAMSON, adjusting dihedral angles is made more intuitive through the Local Move Editor, which provides a simple and interactive way to rotate molecular fragments around bonds using visual widgets. If you’re tired of struggling with manual coordinate entries or jumping between menus, this might be a welcome solution. Here’s how it works.
Using the Local Move Editor
The Local Move Editor (shortcut M) gives you control over translations and rotations based on the local coordinate system (i.e., the internal geometry of your selected atoms or fragment). Here’s what makes it useful for editing dihedral angles:
- Semi-automated bond detection: Simply hover over a bond and SAMSON highlights the associated widgets to rotate the connected fragment.
- Interactive rotation: Use the mouse directly on the bond to adjust the angle in real-time.
To start editing:
- Select a molecule (or a portion of it) using the rectangle or lasso selection tools.
- Activate the Local Move Editor by pressing M.
- Click on the bond you want to rotate around. SAMSON will detect the connected fragment and offer you a curved arrow widget to rotate it.
- Click and drag the widget to rotate the fragment and adjust the dihedral angle directly in the viewport.
Snap to Rotate
If you want more control or intend to align structures, enable rotational snapping in the top-left corner of the viewport or via Interface > Preferences > Editors > Snapping. This allows you to rotate fragments in fixed angular increments (e.g., 10°), making it easier to iterate over conformations.
Why It Matters
Exploring the conformational space of molecules is essential when modeling protein-ligand interactions, searching for low-energy geometries, or building rotamer libraries. The traditional way often involves editing atomic coordinates manually or relying on less visual tools. SAMSON’s Local Move Editor offers a streamlined approach where changes are immediately visible, undoable, and easy to reproduce.
This can speed up workflow for:
- Performing conformational scans
- Adjusting ligand torsion angles in docking studies
- Teaching molecular geometry and rotation concepts
Undo and Repeat with Confidence
All edits performed with the Local Move Editor are part of SAMSON’s undo/redo system. Missed a step? Just hit Edit > Undo. This encourages experimentation without the fear of damaging your molecular model.
Final Tip
If you want even more control, right-click on any widget to bring up a context menu with precise numeric rotation or translation options. Combine this with snapping and you’ll be building your next rotamer library comfortably.
For a full breakdown of SAMSON’s move editors, including global and camera-plane transformations, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.