A molecular project can look complete on your computer and still be difficult to hand off. The structure may be loaded, but supporting scripts, images, research papers, or data can remain in separate folders. When those files are not included with the project, someone opening it elsewhere may need to track them down again.
SAMSON documents offer a practical way to keep molecular work and related materials together: documents can contain molecular models and embed files and folders. Here’s a workflow for bringing structures into SAMSON and making a document more self-contained before you share it.
Start with the structure
Open a local structure using Home > File > Open, or use Ctrl+O on Windows and Linux, or Cmd+O on Mac. SAMSON selects an importer based on the file format. If the importer presents parameters, review them before confirming: defaults are used the first time, and parameters you change are saved for the next use.
You can also fetch structures with the Fetch Structures app, available from Home > Fetch. It downloads structures from the RCSB Protein Data Bank in PDB, mmCIF/PDBx, and MMTF formats. Once imported, the structure appears in both the Document view and the viewport.
Think of the document as the project container
The active SAMSON document is more than a view of the molecule. Its data graph can store atoms, bonds, molecules, models, simulators, and other information. You can inspect its contents in the Document view, opened through Interface > Document view.
Several documents can be open at once, but only one is active at a time. This is useful when comparing or working with different molecules. Before adding supporting materials, check which document is active: new content is added to that document. Switch documents from the Documents list or through Home > Documents; create a separate one with Home > File > New.
Bring supporting files along
SAMSON documents support Universal File Embedding, so they can include Python scripts and other files and folders—not just molecular models. For example, you might keep a relevant image, research paper, data file, or script with the structure it relates to.
To add materials, drag and drop files or folders into SAMSON and respond to the prompt about embedding them. Alternatively, use Home > Embed files or Home > Embed folders. The files and folders are then stored within the document. This makes the document self-contained with respect to the items you embedded, which can make transferring it between computers and sharing it more straightforward.
A quick handoff check
- Confirm the intended document is active before importing or adding materials.
- Check the imported structure in the Document view and viewport.
- Identify any supporting files or folders that belong with the project.
- Embed those items using drag and drop or the Home menu.
- When you are ready to share, continue to the documentation on sharing documents.
Embedding materials does not replace thoughtful project organization, but it can reduce the friction of moving a project when its related files are included in the document. For details on opening structures, documents, and embedding, see the SAMSON loading molecules documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.