One common concern among molecular modelers is project portability. Sharing project files with colleagues, collaborating across institutions, or simply switching workstations often brings up the familiar headache: missing dependencies, broken links, Python files misplaced, or data sets that didn’t make the move. In these situations, managing molecular projects can feel like maintaining a house of cards.
SAMSON tackles this issue with a feature that’s easy to overlook but incredibly powerful: Universal File Embedding. With this, all the files, scripts, folders, images, and even computational tools related to a project can be embedded directly into a SAMSON Document.
Why embedding files matters
Let’s say you’ve created a molecular model and written a custom Python script to analyze interactions. You’ve also compiled a small dataset and included an image to illustrate a particular molecular interface. If you don’t embed all of this into your working document, sharing it becomes complicated. The recipient might get your model, but not the script or dataset. Next thing you know, you’re digging through email threads or cloud folders to piece it all back together.
By embedding files directly into a SAMSON Document, your whole project becomes self-contained. Everything is saved together, allowing smooth transitions between environments and simplifying collaboration.
What can you embed?
Almost anything:
- Python scripts and even whole Python apps (including machine learning apps)
- Structural biology data and analysis results
- Reference publications and supplementary images
- Custom input files, text notes, or configuration settings
How to embed files or folders
Embedding files in SAMSON is straightforward:
- Drag and drop the files directly into SAMSON. You’ll be prompted to embed them.
- Or, from the top menu, follow
Home > Embed filesorHome > Embed folders.
The dialog gives a clear confirmation and allows you to organize content within the document.
Sharing a complete project
Once all components are embedded, your SAMSON Document is ready to be shared or moved. There’s no need to gather and package external files — everything is there.
This is especially handy when collaborating on computational notebooks or using deep learning models for structural predictions. Embedding ensures the entire project is transferred with full fidelity.
Conclusion
If you’ve ever opened a molecular model and wondered, “Where did that analysis script go?” or “Did I forget to include the control dataset?”, embedding files in SAMSON Documents offers a clean solution. It keeps everything neatly in one place, reducing friction when collaborating or moving between environments.
To explore more about loading molecules, working with documents, and managing data in SAMSON, check out the official documentation page: 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.