In molecular modeling, creating accurate and realistic molecular structures can be a challenge. Whether building from individual atoms or larger fragments, ensuring proper orientation and avoiding implausible substitutions are crucial for reliable simulations and analyses. That’s where SAMSON stands out with its intuitive and powerful fragment orientation features, facilitating a seamless building experience for users.
Understanding Fragment Orientation
When connecting molecular fragments, orientation and placement are key to maintaining chemical validity and structural integrity. In SAMSON, the Add editor provides several tools to handle this efficiently. These tools include:
- Predicting fragment orientations: SAMSON automatically positions fragments to avoid overlapping atoms and ensures plausible connections where possible.
- Preventing implausible substitutions: Acceptable substitutions or additions are highlighted with a green overlay, while red overlays indicate forbidden ones.
- Adjusting hydrogens: Hydrogens are automatically added or removed when connecting fragments based on chemical rules.
- Merging overlapping atoms: When fragments overlap, SAMSON intelligently merges atoms to simplify the structure.
All these options can be controlled and customized in the Preferences to align with your specific needs.
Step-by-Step: Orienting Molecule Fragments
To adjust the orientation of a fragment, SAMSON offers powerful move editors:
- After adding a fragment to your molecule, select it in the Document view or directly in the viewport using a selection editor.
- Activate the Local Move Editor (shortcut: M), which allows precise movements and rotations.
- You can specify a pivot atom for rotation. For this, zoom in so the desired atom is visible outside the widget controls, and then click on it to set it as the pivot.
- Use the trackball style controller in the move editor to rotate the selected fragment around the chosen pivot. Dragging any part of the sphere rotates the fragment freely, while the arrows allow for rotation along principal axes for controlled adjustments.
For specific use cases, you can rotate fragments around bonds by simply clicking on the target bond using the Local Move Editor. SAMSON will select the smaller fragment rotationally and display move widgets for targeted edits, as demonstrated here.
Aligning and Distributing Molecules
If you’re working on larger assemblies involving multiple molecular fragments, SAMSON also allows you to globally move, align, and distribute molecules using the Global Move Editor (shortcut: K). This functionality helps create structured systems like molecular arrays without manual errors. Setting a pivot atom and enabling rotational snapping further ensures precision during alignment.
To fully explore SAMSON’s fragment orientation features and improve your molecular modeling projects, check out the detailed Building Molecules guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.