As molecular modelers, we often work with many moving parts: molecular structures, scripts, analysis data, figures, and draft papers. Keeping all of these project components synchronized across machines—or sharing with collaborators—can become an organizational challenge.
Fortunately, SAMSON‘s Universal File Embedding system helps address this issue by allowing you to embed files and folders directly inside your molecular document. This makes your project self-contained and portable—you can literally carry your entire workspace within one .samx file. Let’s take a closer look at how this works.
What is File Embedding?
When you embed files or folders in a SAMSON document, they become part of the document itself rather than being linked externally. This means:
- You don’t have to manage external file paths or relocate assets manually.
- The entire project—including structure files, Python scripts, plots, or even documentation—can be easily shared.
- Everything stays intact when moving to another computer or collaborating remotely.
Embedding Files in Practice
You can embed files or folders in two simple ways:
- Drag and Drop: Just drag a file or folder into the SAMSON application window. You’ll be prompted to choose between embedding it or linking it externally.
- Via the Menu: Use the menu options
Home > Embed filesorHome > Embed folders.
Embedded content is stored inside the document file, so there will be no broken links even if the embedded files are deleted or moved from their original locations.
What Can You Embed?
This is particularly useful if your modeling work involves more than just the molecular structure:
- Python scripts that automate tasks or run simulations
- Machine learning models and associated data
- Experimental data used for comparisons
- Figures and images for publication
- Research notes or articles relevant to your project
These can all be placed alongside your model and accessed directly within the SAMSON interface.
Example: Embedding a Script
If you’ve created a Python script for custom analysis, you can simply drag it into SAMSON. The interface will ask if you’d like to embed it. Once accepted, the script will always accompany your model and can be executed without worrying about external dependencies.
Sharing a Self-Contained Project
Once your file is ready, it can be published or sent to a colleague with confidence that all necessary content is included. Embedded documents are fully supported by SAMSON Connect, where you can choose the visibility and access level when sharing.
Conclusion
If you’ve ever struggled with missing dependencies or incomplete project archives, embedding your assets inside a SAMSON document can simplify your workflow and make collaborative work much easier. It’s a small feature with a big organizational impact.
To learn more about embedding files in SAMSON, refer to the full documentation here: https://documentation.samson-connect.net/users/latest/loading-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.