Managing large molecular design projects often involves juggling multiple structures, scripts, and associated data files. For many scientists and modelers, this can quickly become overwhelming—particularly when trying to locate specific elements, toggle between tasks, or share their work. Fortunately, SAMSON offers a powerful solution through its hierarchical Document system, which lets you structure, visualize, and manipulate your molecular data with surprising flexibility.
At the heart of this system is the Document view, where users can interact with all components of their active project as a dynamic, hierarchical graph. Each document can contain structural nodes (molecules, atoms, residues), folders, files, and more—offering a centralized way to manage everything related to a particular simulation or investigation.
Why Folder Structure Matters
Folders in SAMSON act as containers that help group related elements together. Whether you’re working with a complex protein-ligand system, comparing conformations, or testing different force fields, folders allow you to:
- Apply changes (e.g., hide/show, select) to entire groups of nodes in one click
- Keep your workspace clean and organized
- Embed relevant files—like input data, figures, or documentation—within your project
To create a new folder, navigate to Edit > Folder. Once added, you can drag and drop nodes into folders or nest folders recursively for more granular organization. This is particularly useful when managing different versions of a molecular system or comparing simulation results side-by-side.
Embedding Files: Keep Everything in One Place
Scientific projects often involve a variety of file types—datasets, PDFs, images, scripts—and keeping them tied to a molecular model can be challenging. SAMSON addresses this by allowing users to embed virtually any file directly into a document.
These embedded files are stored within the document itself, creating a self-contained project folder. This means you can send your entire project—along with its associated files—to collaborators or move it between machines without worrying about missing paths or dependencies.
Switching Documents with Ease
You can open and manage multiple documents simultaneously in SAMSON. While only one document is active at a time (visible in the Document view), switching between them is as simple as using the Documents dropdown menu in the top-left corner or navigating to Home > Documents.
This is incredibly useful when comparing results between systems or copy-pasting structures and components from one document to another.
Keep Your Projects Together
The combination of folders and embedded files provides a seamless method to structure your work. For those running multiple simulations or preparing publications, it’s a valuable way to ensure reproducibility and make project handoffs smoother.
Documents in SAMSON offer more than a canvas for molecular models—they’re a flexible workspace aimed at helping scientists manage complexity, stay organized, and ultimately, work more efficiently.
To learn more about how to use documents in SAMSON, visit the official documentation page: https://documentation.samson-connect.net/users/latest/documents/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.