A small edit can have a large effect when it lands on the wrong part of a molecular structure. Perhaps you meant to inspect one residue but selected a larger group, or you want to measure a geometric feature before deciding what to change. In either case, the useful habit is the same: make the target clear before acting, and keep a way to review your steps.
SAMSON’s core document workflow brings together four practical activities: selecting nodes, inspecting their properties, measuring geometry, and using undo and redo. Treat them as checkpoints rather than separate features. Each checkpoint helps answer a different question: What am I working on? What do I know about it? What does its geometry tell me? Can I recover if I need to?
1. Make the target explicit
Start by selecting the nodes relevant to your task. Depending on the work, that might mean atoms, residues, molecules, or other nodes. SAMSON supports selection through commands, editors, filters, or the Node Specification Language (NSL). The important point is not to use every method; it is to choose a selection method that makes the intended scope clear.
Before moving on, pause and state the target in plain language: “I’m working with these atoms,” or “I’m checking this molecule.” If the selection does not match that sentence, correct it before inspecting or editing. This brief check is especially helpful when moving between tasks, because a previous selection may not be the one you need now.
2. Inspect before you edit
Once the target is selected, use the Inspector to check its properties. Inspection gives you an opportunity to confirm what you selected and review relevant information before changing anything. If a property needs adjusting, make the change deliberately, with the selected nodes and the intended result in mind.
A useful pause is to ask two questions: “Are these the nodes I intended?” and “Is this the property I meant to change?” That simple habit separates identifying a target from modifying it. It also makes the workflow easier to retrace if the result is unexpected.
3. Measure when geometry matters
When a decision depends on spatial relationships, measure rather than relying only on appearance. SAMSON’s measuring workflow covers distances, angles, and dihedrals, and measurements can be saved. For example, a distance check can help you record a separation you want to compare later; an angle or dihedral measurement can give you a specific geometric value to refer to while evaluating a structure.
Think of a measurement as a checkpoint, not a verdict. It provides a value you can use in context. If you are comparing or reviewing geometry, saving a measurement can help preserve the result instead of relying on memory.
4. Use history as part of the workflow
Undo and redo let you move backward and forward through document history. That makes history useful not only after a mistake, but also during careful exploration: you can review document changes and return through them as needed. When trying an edit, take a moment afterward to decide whether the result is what you wanted. If not, history is the place to recover and continue from an earlier state.
A practical sequence to keep in mind is select → inspect → measure if needed → edit → review history if needed. Not every task requires every step. A quick property check may not call for a measurement; a geometry check may not involve editing at all. The sequence is a safety net, not a rule that every action must follow.
A compact pre-edit checklist
- Target: Have I selected the atoms, residues, molecules, or other nodes I actually mean to work with?
- Properties: Have I checked the relevant information in the Inspector before changing it?
- Geometry: Would a distance, angle, or dihedral measurement clarify the question?
- Recovery: If the result is not right, do I know to use undo or redo to navigate document history?
This routine helps make molecular work more deliberate without slowing every task down. The goal is simply to catch mismatches early: the wrong selection, an unchecked property, or a geometric assumption that would be better measured.
For the full guide and links to the related workflows, see Work with structures.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.