Collaborative molecular modeling projects often involve more than just structural data: Python scripts, research articles, experimental data, machine learning models, and various other resources contribute to replicability and transparency. But organizing and sharing these assets alongside complex molecular systems tends to be messy.
SAMSON, the integrative molecular design platform, offers a straightforward solution with its Universal File Embedding feature. By embedding files and folders directly into a SAMSON document, users can create fully self-contained projects that are easy to share, archive, and transfer.
Why Embed Files in Molecular Projects?
Whether you’re preparing a project for peer review, collaboration, or teaching, maintaining a consistent set of files tied to your models helps ensure reproducibility. Traditional file management often leads to broken links or missing files when projects are moved or shared.
With embedded content, everything stays in one place: scripts to run analyses, documentation, source data, even figures for publication. SAMSON documents become portable molecular workspaces.
How to Embed Files and Folders in SAMSON
There are two main ways to embed content into a SAMSON document:
- Drag and Drop: Simply drag your files or folders into the SAMSON window. You’ll be prompted to choose whether to embed them or link them externally.
- Menu Navigation: Go to
Home > Embed filesorHome > Embed foldersto insert content explicitly.
Once embedded, all files and folders are stored within the SAMSON document itself. This means:
- Your document is portable; you can move it across systems without losing references.
- Collaborators or reviewers can access every embedded item immediately.
What Types of Files Can Be Embedded?
There’s no restriction on the types of files you can embed. Common use cases include:
- Python scripts or entire Python-based applications for performing analyses or processing results.
- Machine learning models or data pre-processing pipelines used in computational design.
- Literature references and documentation explaining modeling decisions.
- Datasets, logs, or figures related to simulations and experiments.
This approach fits well within research workflows that emphasize transparency and reproducibility—especially in collaborative settings or when preparing data for publication.
Practical Advantages of Embedding
If you’ve ever emailed a colleague molecular files along with a handful of scripts and a README, and then received questions because something was missing or out of sync—embedding can help. It lifts the cognitive burden of tracking external file dependencies and ensures everything travels together, always in context.
Students and educators may also find embedded documents helpful when preparing teaching materials: a complete molecular modeling problem with instructions, data, and tools enclosed in one document file simplifies everything.
To explore more about file embedding and related document-management features, visit the original documentation page: Loading Molecules in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON from https://www.samson-connect.net.