For molecular modelers, building complex structures can often feel like assembling a 3D puzzle with missing pieces. In SAMSON, this challenge is met with an intuitive approach: constructing molecules using fragments. By assembling predefined or user-created assets, you can efficiently create intricate molecular models tailored for your research needs.
The Power of Fragment-Based Building
Fragment-based molecular design allows you to leverage predefined pieces, such as functional groups, rings, or entire molecules, as building blocks for molecular systems. This approach not only accelerates the construction process but ensures accuracy in modeling interactions and geometries. SAMSON provides a vast library of assets accessible via the Asset Browser, and it also enables you to use fragments straight from your workspace.
Getting Started with the Asset Browser
The Asset Browser in SAMSON is your control center for exploring and managing fragments. To begin, navigate through the default assets or use the Filter assets… search bar to find specific fragments. Double-clicking on a fragment activates the Add editor, where you can start incorporating it into your molecular model.
Switch between list and grid views to optimize your browsing experience and, if needed, adjust image and text sizes using Ctrl + mouse wheel.
Constructing with Fragments
To start building, first select the fragment you’d like to use. For example, you can choose a phenol molecule from the Aromatics folder in the Asset Browser. Place the fragment directly into your viewport by clicking, or substitute atoms in your existing structure with the chosen fragment. SAMSON utilizes smart orientation features to ensure seamless integration, preventing implausible substitutions.
Pro tip: Use the Ctrl/Cmd key to modify the substitution atom or bond within the fragment, allowing more control over placement and integration.
Combining and Customizing Fragments
As you integrate fragments, you can further customize them using SAMSON’s interactive minimization (shortcut: Z). This process adjusts geometries in real time, ensuring accurate and realistic molecular configurations. For more advanced edits, you can create your own fragments from existing selections:
- Activate the Add editor or Select editor.
- Select the desired fragment in the Document view or the viewport.
- Right-click and choose Use selection to build.
Final Adjustments
Fragments can be precisely oriented using Move editors. For example, click M to activate the Local Move Editor and set a rotation pivot by clicking on an atom. Adjust rotations using the trackball or axis arrows to refine your model’s configuration. This flexibility ensures all parts of your model align accurately before final optimization.
Conclusion
Fragment-based molecular assembly in SAMSON makes the modeling process intuitive and efficient, providing tools to streamline the design of complex structures. By combining the Asset Browser, Add Editor, and interactive customization options, you can create and refine molecular systems with ease.
To learn more, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at SAMSON Connect.