One common challenge in molecular modeling is organizing all the supporting files around a project. Not just the molecular structures, but also your Python scripts, graphs, notebooks, papers, and other reference materials. Keeping these files in one place—especially when switching computers or collaborating with others—can be a hassle. Often, things get misplaced, projects become disorganized, and sharing turns into a puzzle.
Fortunately, SAMSON offers a built-in feature that tackles this exact pain: Universal File Embedding.
What is Universal File Embedding?
With this feature, you can embed not only molecular structures but any type of file or folder directly into your SAMSON document. Whether it’s a Python script, an image, a simulation input file, or an entire dataset folder, it stays with your document – fully self-contained.
This means that your files travel with your molecular model. Send the document to a colleague, open it on a different device – all your files are there. Everything you need, in one place.
How it works
You can embed files or folders by:
- Drag-and-drop them into the SAMSON interface directly. A dialog will appear asking whether you want to embed the files.
- Using the menu: go to Home > Embed files or Home > Embed folders.
Once embedded, the files become part of the document. You can access them whenever you open the document in SAMSON, even if you’re offline or on a different computer.
Embedding use cases
Here are a few common examples of how Universal File Embedding can be useful:
- Scripts and automation: Store Python scripts used to process or analyze data along with the models they work on.
- Simulation data: Keep configuration files, output summaries, or visualizations directly in the same document as your molecular system.
- Collaboration: Share the entire project, including methods and references, in a single file.
- Archiving work: Make long-term storage of complex projects simpler by ensuring everything is in one place.
Why this helps
In addition to portability, embedding adds a layer of reliability. Your files won’t be moved accidentally, and there’s no need to maintain a separate folder structure. Everything tied to a modeling session becomes reproducible and easier to share.
Interested in learning more about how to embed files in SAMSON? Read the full documentation here: Loading molecules.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.