Molecular modeling projects often grow in complexity over time: multiple molecules, intermediate results, test structures, images, scripts, and embedded data accumulate. It’s easy for things to become cluttered, which can slow down your workflow and make navigation difficult — especially when switching between tasks or preparing files for sharing.
One helpful SAMSON feature designed to address this pain point is the ability to group nodes using folders in documents. If you’re using SAMSON for multi-step modeling tasks or collaborative projects, understanding how to use folders can save you time and help you stay organized.
What can folders contain?
Folders inside a SAMSON document are flexible. You can include any type of node in them — from structural components like atoms and molecules to cameras, scripts, and even other folders. This allows you to:
- Group related molecules together (e.g., molecules in the same pathway or step of a simulation).
- Collect all analysis results in one folder.
- Keep alternative configurations or conformations neatly separated.
- Embed reference documents or images along with the modeling data.
Batch operations
Folders aren’t just containers; they also allow you to apply operations to sets of nodes simultaneously. For example, hiding an entire protein complex across multiple subunits becomes a single click. Similarly, you can apply filters or run Python scripts on a defined subset just by targeting the nodes in a folder.
Making documents self-contained
Embedded folders — and any files they contain — are stored within the SAMSON document itself. This means your document becomes self-contained. When you share or transfer it, there’s no risk of linked resources going missing.
You can embed nearly anything: PDFs, CSV files, Python scripts, images, or even structure files. This is especially useful for reproducibility, collaboration, and archiving workflows for later reuse.
Creating and managing folders
To create a folder in SAMSON:
- Click on Edit > Folder in the menu
- Or use the shortcut:
Ctrl + Shift + Fon Windows/Linux orCmd + Shift + Fon macOS
Once created, you can drag and drop nodes into the folder in the Document view. This interface shows the hierarchical structure of your document and makes it easy to reorganize components as your project evolves.
Folders can contain other folders, allowing you to manage nested groupings. For example, a folder for a molecular system might contain subfolders for input structures, results, and analysis scripts.
Why this matters
If you’ve ever struggled to keep your modeling projects manageable — or shared a document only to realize key data was missing — folders offer a practical solution. They support clear organization, enable batch actions, and ensure self-contained portability of your work.
To learn more about documents and folders in SAMSON, visit the 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.