When working on molecular modeling projects, keeping track of all relevant files—input data, Python scripts, images, papers, notes—can become challenging. Files are often scattered across folders or hard drives, shared by email, or lost in different versions. Wouldn’t it be useful to have everything related to a modeling task embedded in a single file?
SAMSON’s Universal File Embedding provides a surprising and practical solution to this common issue.
Embedding Files and Folders in Your Projects
In SAMSON, you can embed almost any file or folder directly within your molecular model document. This includes:
- Python scripts or notebooks for automation and analysis
- Data files, tables, and graphs
- Images of molecular structures or simulation results
- Even entire Python apps for machine learning integration
This means your SAMSON document is more than just a molecular structure: it becomes a portable project hub.
How It Works
You can embed files or folders in two simple ways:
- Drag-and-drop: Drop any file or folder into the SAMSON window. A dialog asks whether you’d like to embed it or just link to it.
- Menu navigation: Use Home > Embed files or Home > Embed folders.
Submit and your file becomes part of the document. When you save the document, everything is packaged together in one file: molecules, settings, data, and references all travel as a unit.
Why This Helps
The ability to embed files directly into a model file addresses several user challenges:
- Portability: Your entire modeling environment can now live in one file. Moving between computers or sharing with colleagues requires no additional packaging.
- Reproducibility: All parameters and scripts used in the project stay attached to the molecular data, improving reproducibility.
- Collaboration: You no longer need to send separate scripts or folders. Share one SAMSON document, and teammates get everything they need.
Use Cases
Here are some examples where this feature shines:
- Embedding a paper draft with the molecular model it discusses
- Saving a machine learning script that classifies docking poses alongside the dataset it used
- Storing simulation trajectories and setup files with the result structure
Project integrity no longer depends on external file systems or meticulous folder hierarchies.
A Self-Contained Project Model
Thanks to SAMSON’s Document system, your file isn’t just a viewer snapshot—it preserves your workflow, analysis code, and structures. This structure is ideal for ensuring that scientific files remain usable and understandable even weeks, months, or years later.
To learn more about embedding files and folders, visit the SAMSON documentation: https://documentation.samson-connect.net/users/latest/loading-molecules/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.