Working with molecular data often involves handling multiple structures, simulations, and associated files — all within a single modeling session. If you’ve ever felt overwhelmed navigating large molecular models or trying to apply the same operation to a group of molecules, you’re not alone.
That’s where folders in SAMSON documents come into play. Though easy to overlook, this feature can significantly reduce complexity and boost your efficiency when working on sophisticated molecular designs.
Why You Might Need Folders
Imagine you’re modeling a protein-ligand complex and evaluating several conformations, binding sites, or comparative residues. Without proper structure, the document can quickly become cluttered — and selecting or manipulating specific parts can become frustrating.
Folders allow you to structure content logically: you can group molecules by type, function, or workflow stage. Whether hiding groups of nodes or applying batch operations, folders act as containers that make your work more manageable.
How It Works
In SAMSON, folders are simply node containers that reside in your document — meaning they follow the same rules of node hierarchy. You can:
- Group any type of nodes under a folder
- Rename folders to suit your workflow (e.g., “Ligands Batch A”, “Docking Results”)
- Hide or show entire groups instantly
- Apply context actions to entire folders, like calculations or visual changes
To create a new folder, use the menu: Edit > Folder. This adds a new, empty container to your document structure. You can then drag and drop existing nodes into this folder. Organizing models becomes as intuitive as sorting files on your desktop.
Sharing and Portability
When you embed folders with files into your SAMSON document, everything is saved within one self-contained environment. This is especially helpful for:
- Transferring documents between computers
- Sharing models with collaborators
- Archiving your project with all supporting information
You can include not just molecular nodes, but also images, scripts, PDFs, and other supporting files inside folders. This makes your entire modeling process reproducible and easier to revisit in the future.
One Click, Many Actions
Want to analyze all ligands in a large document? Put them in a folder. Need to hide several side chains temporarily? Group and toggle their visibility in one go. SAMSON treats folders like first-class citizens in the document structure — and this means fewer clicks and better focus.
In a field where clarity and reproducibility are essential, small organizational features like folders can give you a clear advantage.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net