Collaborating on molecular modeling projects often comes with a familiar pain: file fragmentation. Between structures, scripts, analysis results, and supporting documents, tracking versions and sharing complete projects can be cumbersome. Ever forwarded a structure file and forgotten the accompanying script? Or received a PDB without knowing which parameters were used to import it? SAMSON has a way around this—through Documents and integrated sharing via SAMSON Connect.
With SAMSON Documents, you can package molecules, models, simulation settings, Python scripts, research data, and even entire folders into a single environment you can reuse and share. This makes collaboration more transparent and significantly reduces the chance of miscommunication or lost information.
What is a Document in SAMSON?
A Document in SAMSON is the main workspace that holds everything you are working on: molecular structures, results, embedded files, etc. Your imported files or constructed molecules live inside this document and are visible in the Document view, where you can inspect the data graph of molecules, nodes, and associated properties.
Why Embedding Files is Useful
Rather than sending raw files separately, SAMSON allows you to embed files and folders directly inside your Document. You can drag and drop them, or use:
- Home > Embed files
- Home > Embed folders
By embedding relevant materials—scripts for analysis, multi-model configurations, even PDFs with research articles—you create a portable, self-contained project. When you move your Document to another computer, everything comes with it.
Sharing Documents through SAMSON Connect
Once your project is ready, you can share it easily using the SAMSON Connect platform. From the interface:
Home > Publish
A dialog prompts you to enter a name, description, and choose the visibility level:
- Public – freely accessible by anyone
- Hidden – accessible via a private link
- Restricted – requires an access permission
Collaborate with Confidence
By packaging your complete modeling environment with structures and scripts, your collaborators don’t just get a snapshot—they get a fully functional setup they can run or extend. This is particularly helpful when preparing academic publications, teaching materials, or project handoffs.
Quick Recap
- Use Documents to organize your work in one place.
- Embed external scripts or data directly using drag-and-drop or the Embed menu.
- Share your work or fetch others’ via SAMSON Connect.
Learn more about working with documents here: 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.