Handing a molecular model to a colleague can involve more than sending a structure file. The notes, reference images, scripts, and supporting data that explain the model may live in separate places. That makes it easy for context to get lost—or for someone opening the model on another computer to have to track down its companion files.
SAMSON documents offer a practical way to keep that context together. A document is a hierarchy of nodes: it can contain molecular structures and other structural nodes, as well as folders, files, scripts, conformations, paths, and cameras. Files and folders embedded in a document are stored within it, so the document can be self-contained and transferred or shared as a unit.
Think of the document as a project container
Instead of treating a document as only the visible molecule, consider what a collaborator needs to understand and continue working with it. You might organize related nodes into folders and embed relevant files—such as a PDF, image, data file, structure file, or script—alongside the model. The documentation describes embedding a broad range of file types.
This does not mean every project needs a complex folder tree. The useful principle is simply to keep related material close to the structures it explains. A clearly named folder can help distinguish groups of nodes, and folders also let you apply actions to a set of molecules—for example, hiding or showing them together.
The Document view is where you can inspect this hierarchy. Open it through Interface > Document view, or use Ctrl+1 on Windows and Linux or Cmd+1 on Mac. From there, you can view the document structure, show or hide nodes, select nodes, filter by node names or with Node Specification Language, and reorganize the hierarchy by dragging and dropping nodes.
Keep separate tasks separate, without losing the ability to compare
If you are working on different molecules or different tasks, SAMSON can have several documents open at once. Only one is active at a time: it is the one shown in the Document view. Switching between documents can be useful when you need to work in separate contexts or copy structures from one document to another. Use the Documents list in the top-left corner of the menu, or go to Home > Documents. The interface also indicates how many documents are open.
To start a fresh document, choose Home > File > New. To return to a recently opened one, choose Home > File > Recent. Once you have a document open, use folders and the Document view to make its contents easier to inspect before sharing it.
A small handoff checklist
- Check the hierarchy: make sure the important nodes are easy to find in the Document view.
- Group related nodes: use folders where they make a set of molecules easier to manage or show and hide together.
- Include useful context: embed files and folders that a collaborator will need alongside the model.
- Review the active document: if several documents are open, confirm you are working in the intended one before organizing or sharing.
These steps do not replace good scientific communication, but they can reduce the amount of separate material a recipient has to locate. A more complete explanation of document contents, folders, files, and navigation is available in the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.