A familiar problem in molecular modeling: the structure is open, but the context around it is scattered. Notes may be in one folder, scripts somewhere else, and several related structures open in separate windows. Later, it can be hard to remember which items belong together—or to hand the work to someone else without also sending a list of extra files.
SAMSON documents offer a practical way to keep related work together. A document is a hierarchy of nodes: it can hold structural elements such as molecules, residues, atoms, and groups, as well as cameras, folders, files, Python scripts, conformations, paths, and other nodes. Thinking of the document as both a molecular scene and an organized project space can make everyday work easier to navigate and share.
Start with the structure, not the clutter
Open the Document view from Interface > Document view, or use Ctrl+1 on Windows and Linux, or Cmd+1 on Mac. The view displays the active document as a data graph, so you can inspect how its nodes are arranged.
This hierarchy is useful when the 3D scene alone is not enough to explain what is in a project. In the Document view, you can inspect the structure, select nodes, show or hide them, filter by node names or with Node Specification Language, and rearrange nodes by dragging and dropping. Context menus and the context toolbar provide actions for selected nodes.
A simple organizational habit helps: make the hierarchy answer the questions you are likely to have later. Which nodes belong to the same group of molecules? Which items should be hidden or shown together? What would a collaborator need to recognize the contents of the document? Folders can group different types of nodes, and let you apply operations such as showing or hiding a set of molecules in one action.
Keep related material with the model
A document can contain files and folders, including PDFs, images, data files, structure files, and scripts. Because these files and folders are stored within the document, the document can be self-contained. That is useful when moving work between computers or sharing it: relevant supporting files can travel with the molecular project instead of remaining in a separate location that may be forgotten.
For a project that has accumulated extra material, create a folder with Edit > Folder and use it to group nodes. You can also embed files or folders in the document. The goal is not to create a complicated filing system; it is to reduce the number of places someone must check to understand the work.
Separate tasks without losing track
Sometimes one document is not the right place for every task. SAMSON can have several documents open at once, while only one is active in the Document view. This makes it possible to keep different molecular tasks separate, or to copy structures from one document to another.
Switch documents from the Documents list in the top-left menu area, or through Home > Documents. The menu also shows how many documents are open. On Windows and Linux, use Ctrl+Tab and Ctrl+Shift+Tab to move between documents; on Mac, use Cmd+Tab and Cmd+Shift+Tab.
When you want a clean workspace for another task, create a document with Home > File > New, or use Ctrl+N on Windows and Linux, or Cmd+N on Mac. To return to a recently opened document, use Home > File > Recent.
The practical takeaway is straightforward: use the document hierarchy to make molecular contents legible, folders to group nodes you handle together, and embedded files to keep supporting material close. When a project is split across tasks, separate documents can help keep those tasks distinct without preventing you from switching between them.
For more details, see the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.