Working with molecular models often means juggling several types of files: structures, scripts, datasets, documents, and even code. Anyone who has ever transferred a molecular project from one machine to another—or tried to share it with a collaborator—knows how easy it is for something to get lost or misaligned. To avoid this, keeping everything bundled together is essential.
That’s where the Universal File Embedding feature in SAMSON comes in. This built-in capability allows you to embed any type of file or folder directly into a SAMSON document, making your molecular modeling projects more portable and much easier to share or archive.
Why embed files?
Typical molecular modeling projects may involve:
- Python scripts for simulation or data processing
- Excel or CSV data tables
- Machine learning models
- PDF reports and research papers
- Related images and figures
With SAMSON, instead of managing these files separately, you can store them all within a single document. That means no more broken links, missing files, or project folders scattered across directories. Everything is self-contained and stays exactly how you left it.
How to embed files and folders
To get started, you have two options to embed content:
- Drag and drop: Simply drag the desired file or folder directly into the SAMSON interface. A prompt will ask if you’d like to embed it. Confirm your choice, and the data is added to your current document.
- Via the menu: Go to
Home > Embed filesorHome > Embed foldersin the SAMSON menu. A dialog will open for selecting your content.
Once embedded, files are fully stored within the document structure. You don’t have to worry about file paths or external dependencies. The document becomes a portable container that includes everything you need to reproduce or continue your work.
Common use scenarios
Universal File Embedding proves useful in many situations:
- Teaching and education: Prepare molecular modeling exercises with all the scripts and sources included for students.
- Replication of results: Share a single file with collaborators or reviewers that includes both data and the workflow logic (e.g., your Python analysis script).
- Archiving projects: Store the entire context of a project to revisit it months or years later without worrying about missing files.
More than molecules
It’s important to understand that SAMSON documents are more than files for visualizing molecules. They include atom and bond data, model metadata, simulation setups, and now arbitrary files organized just like folders in your system. Whether you’re running machine learning on molecular structures or scripting automatic docking tasks, everything can travel with your model.
To learn more about working with embedded files and the broader scope of document functionality in SAMSON, visit the full documentation page at https://documentation.samson-connect.net/users/latest/loading-molecules/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.