One of the key pain points for molecular modelers is adjusting bond orders effortlessly during the molecular design process. Whether you’re tweaking a molecule for a simulation or fine-tuning structures for downstream analysis, inaccurate bond assignments can hinder your workflow. In this blog post, we’ll explore how SAMSON’s Edit bonds feature streamlines the process, enabling precise and efficient bond order modifications.
Interactive Bond Editing Made Easy
SAMSON offers an intuitive tool for modifying bond orders directly within its editor. The Edit bonds feature, accessible via the shortcut B, allows users to interactively manipulate bonds in a way that’s both visual and impactful.
To activate the bond editing capabilities:
- Select the Edit bonds editor by clicking on its icon (
) located in the left-side menu of the viewport or use the B shortcut. - Hover over a bond in your structure to view its current order visually represented.
- Click on the – or + buttons that appear to decrease or increase the bond order, respectively.
Real-time Interaction with Interactive Minimization
While adjusting bonds, the visual feedback is enhanced by SAMSON’s real-time interaction with its minimization tools. For example, if the interactive minimization is enabled (shortcut: Z), the molecule will adjust automatically to reflect a stable configuration based on universal force field principles. This ensures that structural edits maintain consistency and plausibility throughout the modeling process.
Advanced Customization with the Inspector
Need to make nuanced adjustments beyond the interactive tool? The Inspector gives additional control. After selecting a bond in the document, you can change its order or type through precise properties from within the Inspector. Keep in mind, however, that when changing bond orders through the Inspector, hydrogen atoms will not be automatically adjusted.
Why This Matters
Efficient bond editing tools like the Edit bonds feature are essential for anyone working on molecular systems. Whether you are cleaning up imported structures, optimizing a designed molecule, or preparing for simulations, minimizing frustration in these repetitive tasks can significantly enhance productivity. SAMSON ensures that bond changes are both straightforward and visually guided, reducing errors and saving time.
For a detailed walk-through of bond editing and other related functionalities, refer to SAMSON’s Building Molecules documentation.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.*