When working on complex molecular modeling projects, keeping track of your files can quickly become a challenge. Structure files, Python scripts, images, data, analyses—all scattered across different directories. If you’ve found yourself emailing compressed project folders or trying to remember which version of a file goes with which model, you’re not alone.
This is where embedded folders in SAMSON can make a difference. Instead of linking to external files on your computer, you can store everything inside your SAMSON document—neatly, portably, and securely.
Why Embedded Folders Matter
With embedded folders, you can group related nodes and files directly inside your molecular document. Need to run multiple simulations on different molecule sets? Just collect each set in a separate folder. Want to apply changes or analyses to a subset of models? Group them and execute operations with a single click.
Creating and Using Embedded Folders
To create a new folder inside your working document:
- Go to Edit > Folder
- Give your folder a name that reflects its content (e.g., Ligands_Set_3 or Docking_Results)
- Drag and drop any nodes into the folder—molecules, images, scripts, and even additional folders
Folders can also help with visualization. Want to hide or show a particular group of molecules at once? Just toggle visibility at the folder level.
Making Your Work Portable
One significant benefit of SAMSON’s embedded folders is that they make your documents self-contained. Documents with embedded folders and files can be transferred across computers with no risk of missing dependencies. Send one file to your collaborators, and you’re all looking at the same document structure.
This is especially useful if you want to:
- Share a full molecular design project with teammates
- Present your work in a teaching or academic setting with all related data in one file
- Backup your work without having to re-organize scattered files
Practical Tips
- Use folders for functional grouping (e.g., all ligands, all energy minimization outputs, etc.)
- Embed reference papers, charts, or spectra by simply dragging the files into the folder
- If you’re preparing presentations, keep your rendered images and viewpoints inside the same document
Once you start working with embedded folders, managing larger projects becomes smoother and more traceable. Every visual, analysis, or script lives inside one place—your SAMSON document.
To learn more, visit the original documentation page: https://documentation.samson-connect.net/users/latest/documents/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.