If you’re a molecular modeler, you know that constructing or modifying molecular systems can be time-consuming and intricate, especially when you’re starting from scratch or making complex edits. Fortunately, SAMSON offers a highly efficient tool to help simplify this process: the Add Editor. In this post, we’ll walk through how to use this editor to build molecules quickly and effectively, addressing one of the most common challenges faced by molecular designers.
Why the Add Editor is Useful for Molecular Modelers
Building molecules often involves placing atoms, functional groups, or entire fragments precisely in a 3D space. Errors can lead to implausible structures or lengthy rework. The Add Editor in SAMSON allows you to streamline the process with several great features:
- Predictive placement for fragment orientations.
- Automatic hydrogen adjustment to maintain chemical correctness.
- Options to prevent implausible substitutions.
- Flexible structure assembly from both individual atoms and pre-built fragments.
Step-by-Step Guide to Building Molecules with Atoms
Building molecules from atoms is an essential skill for many use cases. Below are key actions you can perform:
1. Start with Simple Atom Placement
When using the Add Editor (
), you have quick access to commonly used atoms like hydrogen, oxygen, nitrogen, and carbon. In the Asset Browser, click on an atom (e.g., C) and place it anywhere in the viewport. SAMSON automatically adds the necessary hydrogens to complete the atom’s valence structure.
2. Connecting Atoms
To link atoms together, you can either:
- Substitute an atom: Hover over an atom you want replaced and click it. The bonded atom will be automatically positioned based on covalent radii.
- Create a new bond: Click and drag from one atom’s position to another. This flexibility ensures you maintain control over the molecular assembly.
Here’s how substitution works in action:
3. Modify Bonds and Charges
You can change bond orders interactively with the Edit bonds editor (
). Select the editor, hover over a bond, and use the + and – buttons to modify bond order.
Similarly, you can modify atom formal charges using the Edit charges editor (
). Hover over an atom to adjust its charges interactively.
Building with Fragments
Sometimes, individual atom placement isn’t enough, especially when dealing with repetitive or pre-existing molecular groups. Using the Asset Browser, you can add fragments such as aromatic rings or functional groups. For example, you can find phenol under the “Aromatics” folder and build benzene derivative compounds with ease.
Reusable Fragments
If you’ve constructed a custom fragment, select it, right-click, and choose “Use selection to build” from the context menu. Hold Ctrl or Cmd to choose a substitution atom for seamless integration into new structures.
Minimizing Geometry on the Fly
SAMSON allows for interactive minimization during molecule construction to improve the geometry continuously. Just press Z to toggle minimization on or off and observe your structure optimize in real time as you build.
Conclusion
With SAMSON’s Add Editor, you have all the tools necessary to build accurate molecular models more efficiently and less error-prone. From individual atoms to reusable fragments, SAMSON empowers molecular designers to focus more on their science and less on tedious assembly tasks.
Learn more by visiting 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 get SAMSON at https://www.samson-connect.net.