If you’ve ever found yourself overwhelmed by layers of molecules, multiple structure files, and scattered Python scripts inside your molecular modeling environment, you’re not alone. As projects grow in complexity, so does the challenge of keeping your data manageable. That’s where folders in SAMSON come in handy.
Folders in SAMSON documents offer a simple, practical way to organize your molecular modeling work. Just like on your computer, they allow you to group related items to keep your document structure clear and actionable. But unlike standard file systems, folders in SAMSON aren’t just for visual tidiness—they’re functional elements of your scientific workflow.
Why folder organization matters
A single SAMSON document can contain molecules, residues, atoms, camera views, scripts, conformations, and more. Over time, this can become a forest of nodes that’s hard to navigate.
Using folders lets you do things like:
- Group molecules used for the same simulation or analysis step
- Apply bulk operations (e.g. hide, show, or delete) to a full group at once
- Separate experiment variations (e.g. different ligand configurations) into their own spaces
- Store embedded files (PDFs, images, scripts) in themed collections inside your document
Creating a folder in SAMSON
To create a new folder, go to Edit > Folder. Folders can contain any type of SAMSON node—from atoms to data files—and even other folders, allowing for nested hierarchies.
Once you’ve created your folder, you can:
- Drag and drop nodes into it from the Document view
- Rename it to reflect its contents
- Right-click to apply actions like hiding or locking all contents within
Folders travel with your documents
Folders and embedded files are saved inside the SAMSON document itself. This turns each document into a self-contained project space. When you send a document to a colleague or move it to another computer, all its contents stay together—no missing files or broken links.
This makes it easy to collaborate on complex molecular design work. For example, one document might contain an entire protein-ligand study, complete with molecule structures, simulation scripts, analysis charts, and references—all grouped into folders like “Molecules,” “Scripts,” “Figures,” and “Notes.”
A small trick to work smarter
Instead of relying on separate folders on your operating system, consider keeping all resources linked to a project inside the document itself, using SAMSON folders. This minimizes organizational overhead and lets you focus more on your science and less on hunting files.
To learn more, visit the full documentation at https://documentation.samson-connect.net/users/latest/documents/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.