A molecular modeling project rarely consists of a structure alone. There may be several molecules, scripts, images, PDFs, and other files to keep track of. When these are scattered across folders—or when the document’s hierarchy becomes hard to read—it can take time to find the right item or explain the project to a collaborator.
SAMSON documents can help keep this work together. A document stores a hierarchy of nodes, which can include structural elements such as molecules, residues, atoms, and groups, as well as cameras, folders, files, Python scripts, conformations, and paths. You can also embed files and folders in the document. Since those embedded items are stored within it, the document can be self-contained and easier to transfer or share.
Start with the document view
The Document view displays the active document as a data graph: a hierarchical view of its contents. Open it through Interface > Document view, or use Ctrl+1 on Windows and Linux or Cmd+1 on Mac. From this view, you can inspect the structure, select nodes, show or hide them, and reorganize the hierarchy by dragging and dropping nodes.
This view is useful not only for locating objects, but also for checking whether the document is arranged in a way that makes sense to someone who did not build it. A practical habit is to pause before sharing and inspect the hierarchy: are the important structures easy to find, and are related items grouped together?
Use folders to make groups easier to manage
Folders let you group different types of nodes. For example, you might place related molecules together so you can work with that set as a unit. SAMSON supports applying operations to sets of molecules, including showing or hiding them in one click. To create a folder, choose Edit > Folder.
Think of folders as a way to make the document’s organization reflect the way you work: separate related groups, keep supporting items together, and make it easier to find what you need later. The exact grouping will depend on the project; the useful test is whether the arrangement helps you understand and navigate the document.
Keep supporting files with the project
A document can contain embedded files such as PDFs, images, data files, structure files, and scripts. Folders can also be embedded. Keeping these materials in the document reduces the chance that a collaborator receives a molecular structure but not the supporting information needed to interpret it. It also means the document can be transferred between computers with its embedded contents.
Before sharing, consider which files belong with the project and embed those that another person may need. The goal is not to put every file you own into one document; it is to keep the relevant context close to the molecular work. For details on embedding, see Embedding files and folders.
Keep separate tasks separate
You can have several documents open at once, but only one is active at a time—the one shown in the Document view. Separate documents can be useful when working on different molecules or when you want to copy structures from one document to another. Switch documents using the Documents list in the top-left corner of the menu, or through Home > Documents. To start fresh, choose Home > File > New; recently opened documents are available through Home > File > Recent.
A small organizational check can save time later: confirm the active document, review its hierarchy, group related nodes, and embed the supporting files that should travel with it. For more details, see the SAMSON documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.