For molecular modelers, one of the recurring challenges is quickly assembling complex structures from scratch or existing fragments. Whether you’re working on small organic molecules, nanoparticle systems, or material science, the process of building reliable molecular systems can sometimes feel like a juggling act, especially when dealing with a variety of atomic arrangements. Here, we explore how SAMSON’s Asset Browser can streamline this process, allowing you to focus on understanding and modeling systems rather than tedious construction tasks.
What is the Asset Browser?
The Asset Browser in SAMSON serves as a tool to access a wide range of structural building blocks. These “assets” include individual atoms, functional groups, rings, radicals, entire molecules, and even specialized structures like nanoparticles and 2D materials. Assets can be used to construct molecular systems directly in the SAMSON Viewport.
The great appeal of the Asset Browser lies in its rich library and intuitive search functionality. Need a phenol molecule? How about a fragment of graphene? With a few clicks or a keyword query, you’re ready to add these to your molecular model.
Getting Started with the Asset Browser
To access the Asset Browser, activate the Add editor (A or via the side menu). Then, navigate through the folders of included assets or use the “Filter assets” function at the top of the browser to find exactly what you need. The Aromatics folder, for instance, contains assets like phenol, which you can incorporate into your models by simply clicking or dragging them into place.
Changing your view preferences is straightforward too: Zoom in/out with Ctrl + mouse wheel, or toggle between list and grid modes for a more comfortable browsing experience. For more detailed visual control, you can opt for the magnifying glass icons for zooming.
Building Molecules: An Example
For a hands-on demonstration, consider this example: constructing Bisphenol A (BPA).
- Start by building a propane molecule (C3H8) using the individual carbon atoms in the Asset Browser.
- Switch to the phenol asset from the Aromatics folder. You can modify the atom used for substitution by holding Ctrl and clicking your desired atom on the asset (e.g., the carbon).
- Substitute two hydrogen atoms of the central propane carbon with phenol fragments. SAMSON’s smart fragment orientation will automatically ensure that the additions are well-positioned to avoid implausible overlaps.
- Finally, apply interactive minimization (Z in the Viewport) to refine the geometry.
Check out the visual representation below to see the process in action:
Additional Features for Enhanced Control
If you’d like even finer control, SAMSON allows you to tweak fragment orientation using its Move editors. You can rotate fragments around specific bonds or manipulate them relative to a custom pivot point, ensuring your assembly is optimized for analysis and simulation.
Moreover, if you’d like to incorporate assets from your own library into SAMSON, simply reach out to the team. This added flexibility makes the Asset Browser ideal for more customized modeling workflows.
Learn more about building molecules in SAMSON to discover other advanced tips and tricks.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get started today by downloading SAMSON at this link.