A molecular model can look complete on screen and still be difficult to hand off. The structure may be only one part of the work: useful context can also include scripts, images, PDFs, data files, and other resources. If those pieces are scattered across folders on one computer, a colleague may receive the model without everything needed to understand or continue the project.
SAMSON documents offer a practical way to organize that work. A document is a hierarchy of nodes, which can include structural elements such as molecules, residues, atoms, and groups, as well as folders, files, cameras, scripts, conformations, and paths. In other words, the document can hold both the molecular structure and related project material.
Start with a structure you can inspect
The Document view displays the active document as a data graph. Open it through Interface > Document view, or use Ctrl+1 on Windows and Linux and Cmd+1 on Mac. From this view, you can inspect the hierarchy, select or show and hide nodes, filter nodes by name or with Node Specification Language, and change the structure by dragging and dropping nodes.
This hierarchy is useful for more than tidiness. Clear groupings make it easier to find the parts of a document, and the context menu and context toolbar provide actions for particular nodes. A document that is understandable to its author is also easier for someone else to navigate.
Group related nodes, then keep supporting files close
Folders in a document can group different types of nodes. For example, you might use folders to separate sets of molecules or to keep related items together. They also let you apply operations to a set of molecules, such as showing or hiding them in one click. Create a folder with Edit > Folder.
You can also embed files and folders in a document. The documentation lists PDFs, images, data files, structure files, and scripts among the file types you can embed. Because embedded folders and files are stored within the document, the document can be self-contained and transferred between computers or shared. This reduces the chance that useful project context is left behind in a separate location.
A straightforward handoff habit is to review the document before sharing: check that its node hierarchy is understandable, group related nodes where helpful, and embed the supporting files that belong with the work. This is an organizational practice, not a substitute for checking the contents of a document—but it gives recipients one place to look for the model and its associated materials.
Keep separate tasks separate
You can have several documents open at once, although only one is active at a time. The active document is the one shown in the Document view. Switching documents is useful when working with different molecules or copying structures between documents. Use the Documents list in the top-left menu area or choose Home > Documents. To start a fresh document, choose Home > File > New; recently opened documents are available through Home > File > Recent.
When the project is organized and its supporting material is embedded, sharing becomes less dependent on remembering which files were stored elsewhere. For details on documents, folders, and files, visit the SAMSON documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.