If you’re a molecular modeler, you’ve likely faced challenges when trying to build custom molecular systems efficiently. SAMSON’s Add Editor could be the tool you’ve been searching for. Designed to simplify molecule construction with atoms and fragments, the Add Editor combines precision, interactivity, and speed—transforming a tedious task into an intuitive and enjoyable process.
Create Molecules with Ease
In SAMSON, molecular building begins with the Add Editor. You can construct everything from simple molecules to complex systems using individual atoms, rings, or fragments from the Asset Browser or the Periodic Table. Interactive features like snapping options ensure added components fit seamlessly into your existing structures.
Here is an example of constructing a basic N-acetyl group using the Add Editor:
Smart Building Features
The Add Editor incorporates handy features that solve common molecular-building pain points:
- Automatic adjustment of hydrogens: Avoid manually recalculating hydrogens! The Add Editor adapts hydrogens automatically for new atoms or fragments based on chemical valences.
- Fragment orientation prediction: When adding fragments, SAMSON predicts their best orientation to prevent spatial clashes with the existing structure.
- Prevent implausible substitutions: The editor provides immediate feedback, showing green for valid operations and red for prohibited ones.
Want to place a new atom precisely? Override automatic placement anytime by holding the Shift key to select the exact location or bond of your choice.
Interactive Minimization for Real-Time Feedback
One of SAMSON’s standout features is interactive minimization, which adjusts molecule geometry as you build. Running the minimization feature (shortcut: Z) lets you spot and correct structural issues early in the process. This ensures your molecule remains chemically plausible throughout construction.
With interactive minimization turned on, connecting atoms or substituting fragments becomes a dynamic experience:
Edit Bonds and Charges with Precision
Beyond adding atoms, the Add Editor supports fine-tuning of molecular details. Use the Bond Editor (shortcut: B) to alter bond orders interactively by hovering over bonds and clicking the respective buttons. Adjusting formal charges on specific atoms is equally easy via the Charge Editor (shortcut: C), enabling seamless control over a molecule’s electronic structure.
Switch to Fragments for Faster Assembly
For more complex designs, building with molecular fragments from the Asset Browser accelerates workflows. Fragments are reusable sets such as functional groups, rings, or even entire molecules. You can also create custom building blocks by selecting parts of an existing structure and designating them as fragments. This flexibility makes scaling up your molecular models highly efficient.
Start Building Smarter
The Add Editor removes frustration from molecule construction by providing tools that prioritize precision and interactivity. Whether you’re assembling compounds from scratch or integrating fragments into pre-existing models, SAMSON is designed to streamline your workflow.
Explore more detailed guidelines and tutorials in SAMSON’s full documentation here: https://documentation.samson-connect.net/users/latest/building-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it now at SAMSON Connect.