A small change to a molecular structure can be easy to make—and surprisingly hard to evaluate if you are not sure which atoms or residues were involved. Perhaps you meant to inspect one part of a system but selected a larger group, or you want to check a geometric relationship before deciding what to edit. A deliberate sequence helps reduce this uncertainty: select, inspect, measure if needed, and use document history when you need to step back.
This workflow is useful whether you are learning SAMSON or returning to a structure after some time away. It is not a substitute for understanding the effect of a particular modeling operation. Instead, it helps you establish what you are working on before moving forward.
1. Start by defining what you mean to work on
Before checking a property or making an edit, identify the relevant nodes in the document. Depending on your task, that might mean atoms, residues, molecules, or other nodes. SAMSON provides several ways to select nodes, including commands, editors, filters, and the Node Specification Language (NSL). Choose the approach that fits the selection you need.
The important habit is to treat selection as a question: What exactly do I want the next action to apply to? If the answer is a particular residue or group of atoms, make that scope clear before continuing. This can prevent a common source of confusion: seeing an unexpected result and not knowing whether it came from the operation or from selecting the wrong nodes.
For the selection tools and approaches, see Selecting.
2. Inspect before you edit
Once the relevant nodes are selected, use the Inspector to check their properties. Inspection gives you a chance to confirm that you are looking at the intended part of the structure and to review the properties relevant to your task. If a property needs adjustment, make the change only after you have established which nodes it concerns.
This pause is especially useful when moving between tasks. A selection made for one purpose may not be the right selection for the next. Rechecking the selected nodes and their properties is a simple way to avoid carrying an old assumption into a new action.
Learn about checking and editing properties in Inspecting.
3. Measure when a visual impression is not enough
When a question is geometric, use a measurement rather than relying only on how the structure looks on screen. SAMSON measurements can be used for distances, angles, and dihedrals, and measurements can be saved. These checks can help you record a value you want to refer to while continuing your work.
A practical sequence is to decide what geometric relationship you need to evaluate, select the relevant nodes, and then create the corresponding measurement. Keeping the measurement tied to a clear question—such as checking a distance or an angle—makes the result easier to interpret later.
For details, see Measuring.
4. Use history as part of the workflow
Undo and redo are useful when you are exploring a change and want to recover from a mistake or move back and forward through document changes. Think of history as a safety net for trial and error, not as a reason to skip checking your selection or understanding what an operation does.
If you are about to try an edit, make a habit of checking the target first. If the result is not what you intended, use document history to move back through the change. When you are unsure how history fits into your workflow, review History: Undo and redo.
A compact pre-edit checklist
- Target: Have I selected the nodes that match the question I am asking?
- Properties: Have I checked the relevant properties in the Inspector?
- Geometry: Would a distance, angle, or dihedral measurement help verify what I am seeing?
- Recovery: Do I know how to use undo and redo if I need to revisit a change?
This sequence turns structure work into a series of smaller, easier-to-check decisions. Select the target, inspect it, measure when geometry matters, and use history to recover when necessary. For the full overview and links to the related workflows, learn more in Work with structures.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.