Working with complex molecular models often leads to cluttered workspaces full of multiple molecules, scripts, visualizations, and data files. Over time, it becomes harder to keep track of what’s relevant, what belongs together, and how to perform operations on multiple elements at once. For many molecular modelers, the lack of effective project organization is a recurring pain point.
Folders in SAMSON offer a structured way to tackle this common issue. By grouping related nodes—like molecules, atoms, paths, or even embedded files—into folders, users can simplify their workflow, reduce visual noise, and focus on specific tasks or molecular assemblies more effectively.
Why folders can significantly improve your workflow
In SAMSON, a document is a container for all project-related nodes. As your project expands, you might add dozens or hundreds of individual nodes. Without organization, selecting or hiding specific molecules—or running batch operations—can become tedious. Folders solve this by allowing you to:
- Group related nodes together (e.g., different chains of a protein, ligands, solvent molecules)
- Apply actions to the entire group at once, such as hiding/showing or transforming them
- Keep scripts, structure files, and documentation in one self-contained bundle
How to create and use folders
Creating a folder in your SAMSON document is simple:
Go to Edit > Folder. This will add a new folder node to the data graph in the Document view.
Once created, you can drag-and-drop any node into the folder. This includes molecules, paths, Python scripts, embedded files, and more. Folders help keep everything in logical places, avoiding the typical chaos of large molecular projects.
Use case: one-click visibility control 🔍
Suppose you’re working on a multi-ligand docking study. By placing all ligands in one folder and the receptor in another, you can quickly toggle their visibility for comparison or editing. Right-click the folder and choose Show or Hide All. No need to click on each node individually.
Transferring projects? Folders keep everything intact
Folders in SAMSON are also portable. When you save your project, everything inside the document—including all folders and embedded files—is saved in a single entity. Moving a project to another computer or sharing with collaborators doesn’t require remembering where your external files are; everything is already bundled.
Embedding files inside folders
You can also drag PDFs, images, data files, and scripts into your folders. This turns your SAMSON document into a genuine project container where everything from raw data to analysis code resides alongside your structural models.
To learn more about documents and folders in SAMSON, visit the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at https://www.samson-connect.net.