When working with molecular models, especially across multiple projects or complex molecular systems, keeping your workspace clean and organized can be a real challenge. Structures, scripts, data files, different conformations—everything can pile up quickly. If you’ve ever struggled with finding that specific molecule or keeping related items together, you’re not alone.
SAMSON, the integrative platform for molecular design, offers a helpful solution that many users might have overlooked: using folders within documents to group and manage nodes. This feature is especially useful for those working with detailed systems or handling several tasks in parallel.
What are folders in SAMSON?
In SAMSON, a document is essentially a hierarchy of nodes that includes molecules, atoms, scripts, files, and more. Inside these documents, you can create folders—just like on your computer—to better manage and structure your data visually and functionally.
Folders let you:
- Group any types of nodes together (atoms, molecules, scripts…)
- Hide or show entire groups with a single click
- Apply operations to a group, such as transformations or visual changes
- Further organize your project into logical sections
Creating folders
To create a folder:
- Go to Edit > Folder
- Or use the keyboard shortcut
Ctrl + Shift + F(Windows/Linux) orCmd + Shift + F(Mac)
This adds a new folder to your document in the Document view. You can drag and drop nodes into it, rename it, and perform actions on it just like a regular entity.
Why use folders?
Here are some scenarios where folders can make a difference:
- Multi-complex systems: Working on a protein-ligand system with multiple ligands? Group each ligand and its associated calculations in separate folders.
- Conformational studies: Store conformations or alternative structures in folders labeled by experimental condition or time step.
- Teaching and collaboration: Preparing a file to send to collaborators or students? Folders let you make your document more understandable and easier to navigate.
- Script libraries: Keep Python scripts inside a folder and reuse them across sessions without digging through your file system.
Embedded folders and portability
One of the nicest features is that folders and files you embed into the document are saved within the document. That means your document becomes self-contained—you don’t need to worry about missing file paths or re-linking external documents when you move SAMSON files across computers or share them with peers.
This is especially helpful during collaboration, teaching, or switching between workstations.
Conclusion
If you haven’t used folders in your SAMSON documents yet, try adding a few to your next project. A little bit of structure can go a long way when you’re working at the molecular scale.
To explore more about document organization in SAMSON, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON from https://www.samson-connect.net.