When working on complex molecular modeling projects, keeping all your related files—scripts, datasets, and supplementary materials—organized and in the right place can be a challenge. Molecular modelers often juggle structural data, downloadable database entries, computational scripts, and even research papers across multiple directories and machines. This decentralization can be frustrating, especially when sharing or re-accessing the project weeks or months later.
SAMSON, the integrative molecular design platform, offers a simple yet powerful solution: Universal File Embedding. With this feature, you can embed essentially anything—Python scripts, folders, documents, images, and more—into your active modeling document, keeping everything bundled and portable.
What Exactly Is Embedded?
Embedded files and folders become part of the SAMSON document itself. That means whether it’s a Python-based analysis script, a supplementary CSV dataset, or an image supporting your model, it travels with the document wherever it goes. Once embedded, there’s no longer any risk of a missing dependency or lost file when you revisit your project or share it with collaborators.
Why Embed?
- Reproducibility: Keep all inputs and analysis methods linked to your model.
- Portability: Move your complete project easily between machines.
- Simplicity: Centralize related materials.
- Collaboration: Share documents that are self-contained, clear, and complete.
How to Embed Files and Folders
You have two main options to embed content into a SAMSON document:
- Drag and Drop: Simply drag files or folders into the SAMSON window. You will be prompted to choose whether to embed them.
- Menu Access: Go to
Home > Embed filesorHome > Embed folders.
This intuitive approach works whether you’re embedding a single file or an entire folder.
A Common Use Case: Python Scripts
Modelers who use Python to manipulate structures or analyze results can embed their custom scripts directly into the document. When the document is shared, recipients can review, run, or extend the script without searching for or recreating it. This is especially useful for workflows involving machine learning apps or automated structural analyses.
Making Your Documents Easy to Distribute
Because embedded files are stored within the SAMSON document itself, your project is entirely self-contained. When you’re ready to share your work, you don’t have to bundle extra folders or explain directory setups. Just share the document.
Embedded content is preserved across different computers and operating systems, making it an excellent solution for academic labs, remote collaboration, and reproducible science.
Learn more on the official documentation page: Loading molecules – SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.