When collaborating on molecular modeling projects, one quiet frustration for researchers is project portability—specifically, making sure nothing essential is left behind when sharing a molecular model with a colleague or switching from one computer to another.
Whether you’re creating a simulation, preparing a publication, or building a custom Python-based app, it’s common to end up with a folder full of related files—scripts, PDFs, datasets, screenshots, and more. Losing context or misplacing inputs can disrupt your workflow or delay collaboration.
This is where SAMSON’s file embedding can be helpful.
Universal File Embedding in SAMSON
SAMSON allows users to embed files and folders directly into a molecular project, also known as a document. This means any file—Python scripts, instructions, sample datasets, even entire folders containing supporting material—can be permanently stored within the molecular project.
The key benefit? The SAMSON document becomes completely self-contained. When you send your modeling project to someone else, or transfer it to another machine, you don’t need to worry about missing files:
- Python scripts for automation or analysis
- Documentation or research papers
- Images, figures, or snapshot directories
- Machine learning models trained on biomolecular datasets
How to Embed Files in a SAMSON Document
There are two main ways to embed files or folders into your document:
- Drag and Drop: Drag files or folders from your operating system directly into the SAMSON interface. A prompt will ask if you’d like to embed them.
- Menu Navigation: Use Home > Embed files or Home > Embed folders to manually select the files you want to include.
Files and folders you embed will be shown in the document view, along with your molecular models. They become a part of the data hierarchy, just like atoms, bonds, or simulators.
Why Embedding Can Save Time (and Stress)
Rather than zipping folders and including README files to explain what’s what, embedding creates tidy, all-in-one documents. This is especially helpful for:
- Teaching: Distribute completed model + script + assignment sheet in one file.
- Collaboration: Share rich project data with annotations and references embedded.
- Version tracking: Retain older scripts and notes right inside the model when iterating.
- Offline access: Work effectively without need to sync files across systems.
This makes SAMSON particularly versatile for sharing well-packaged projects or preparing long-term reproducible models.
More Than Molecules
Because documents can now carry not just molecules but also metadata, images, and computational tools (like Python apps), they’re starting to fulfill another important role: not just being containers of 3D structures, but becoming complete molecular research capsules.
To learn more about embedding files and other document features, 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 download SAMSON at https://www.samson-connect.net.