When working with complex molecular models and simulations, keeping everything organized is not a luxury—it’s a necessity. Whether you’re comparing different ligands, running multiple simulations, or collaborating with others, your data needs to be structured and accessible. This becomes trickier when you’re dealing with dozens of molecules, scripts, and related datasets all in a single project. If you’ve ever found yourself lost in a sea of atoms and files, you’re not alone.
That’s where folders in SAMSON documents come in. With SAMSON’s folder system, you can intuitively organize your molecular structures, scripts, and even embedded files—directly inside your document—making your project self-contained and easier to manage.
Why Folders Matter
A SAMSON document stores many different types of nodes: molecules, atoms, scripts, cameras, paths, and more. As your project grows, the document can get quite crowded. Organizing content into folders helps you:
- Group related molecules or structures together (e.g. all ligands, all receptors).
- Apply actions (like hiding or showing) to an entire group in one click.
- Embed related files (scripts, data tables, PDFs) in a self-contained way.
- Keep your workspace clean and improve navigation.
Creating a Folder
To create a new folder inside a SAMSON document, just go to Edit > Folder in the top menu. Once it appears in your Document View, you can drag-and-drop any nodes into it. This is especially useful when you want to apply collective actions—like turning off the visibility of an entire group of molecules.
Folder Power: Embedding Files
Folders aren’t just for molecules. You can also embed various file types directly inside SAMSON documents, such as:
- PDFs (experimental protocols, references)
- Images (molecular diagrams, figures)
- Structure files (other molecules, docking results)
- Scripts (Python workflows, analysis scripts)
These files are then saved inside the SAMSON document, making it self-contained. This means you can easily share the entire document—including all its contents—with a colleague or move it to another computer without worrying about missing files. Just one file, no dependencies.
Use Case: Sharing a Project
Let’s say you’re researching multiple inhibitors for a given protein. You can create separate folders to store:
- Each inhibitor and its docking pose
- Analysis scripts
- Relevant literature in PDF format
Everything remains in one single document, neatly separated by folders. When it’s time to share your work or return to it a few months later, everything is where you left it. No more wondering where you saved that script or which version of the molecule structure you used.
Key Takeaways
- Folders help declutter your document and streamline workflows.
- You can embed files and make your document self-contained.
- It simplifies collaboration and long-term project maintenance.
For molecular modelers dealing with complex projects, this is a small change that can make a big difference.
To learn more, visit the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.