Handling large molecular systems often means dealing with hundreds or even thousands of individual structural components—molecules, residues, atoms, and sometimes metadata or scripts. Keeping track of them all while maintaining focus on your modeling goal can quickly become overwhelming. This is especially true when your workflow requires comparing molecular structures, hiding and showing elements selectively, or sharing your project across teams. Fortunately, SAMSON offers an elegant solution: document folders.
Folders in SAMSON allow you to group different types of nodes—molecules, paths, scripts, conformations—into neatly organized containers. You can use these folders to:
- Group molecules into functional or structural sets
- Apply visibility settings to whole groups at once
- Enable or disable computational actions on multiple components
- Embed and organize supporting files like PDFs, scripts, or raw data
This might seem like a basic feature, but it addresses a persistent pain point for molecular modelers: keeping projects clean and manageable, especially when switching between tasks or collaborating across systems.
Creating and Using Folders
Creating a folder is straightforward: go to Edit > Folder. This adds a new folder node to your active document. You can then drag and drop relevant nodes into the folder.
Once created, folders behave like any other node in SAMSON’s Document view. This means you can:
- Rename your folders for clarity
- Control visibility settings via the right-click context menu
- Child folders and nested structures to further refine your organization
Self-contained Project Files
Perhaps one of the most useful aspects of folders in SAMSON is that they can contain files. Imagine you’re preparing a molecular model alongside an analysis PDF, a Python simulation script, and a set of experimental spectra images. You can store them all inside your SAMSON document, using folders to organize them logically.
This makes your project entirely self-contained: you won’t have to zip extra folders or write long email instructions saying “Don’t forget to include the XYZ.csv file!” Everything travels as a single file.
When and Why to Use Folders
Here are a few scenarios where folders can become a critical organizational tool:
- Multi-target projects: Organize each target in its own folder, complete with input files, simulation results, and annotations.
- Comparative modeling: Use folders to group different conformations or molecular variants.
- Teaching and collaboration: Store explanations and resources directly with the project.
- Script-based analyses: Include scaffolding Python files in the folder where they’re used.
Ultimately, document folders in SAMSON are more than just a tool for cleanliness—they help you think in terms of projects rather than raw files and nodes. This shift is particularly valuable when models grow in complexity or must be communicated clearly to others.
To learn more about working with folders in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.