A small mistake in a molecular model can be hard to notice once you have moved on to building, analysis, or presentation. You may have selected a larger part of the structure than intended, inspected the wrong node, or made a change and then forgotten exactly what it affected. A short checking routine helps make exploration more deliberate—and makes it easier to recover when an experiment does not go as planned.
In SAMSON, a useful sequence is select, inspect, measure, and review history. These steps address different questions: What am I working on? What properties does it have? Does its geometry meet the check I need? And can I retrace a change?
1. Select the thing you mean to work on
Start by identifying the nodes relevant to your task. Depending on what you need, that may mean atoms, residues, molecules, or other nodes. SAMSON provides several ways to select nodes, including commands, editors, filters, and the Node Specification Language (NSL).
It is worth pausing after selection to ask whether the selection matches the scope of your intended action. If you want to inspect one node, a broad selection may make the next step confusing. If you are comparing or measuring several parts, selecting too narrowly may leave out what you need. Treating selection as a deliberate first step reduces the chance that later inspection or editing is based on the wrong target.
2. Inspect before changing properties
Once the relevant nodes are selected, use the Inspector to check their properties. This gives you a chance to understand what is currently selected before adjusting anything. When you do edit a property, make the change with a specific question in mind: which node or nodes should it affect, and what do you expect to learn or accomplish?
This is especially useful when you are still getting familiar with a structure. Separating inspection from editing makes it easier to notice whether a value was already present or whether it changed during your work. If the result is unexpected, you can return to the selection and property check rather than guessing at what happened.
Read about inspecting properties.
3. Measure geometry when visual judgment is not enough
A structure can look plausible on screen while still needing a precise geometric check. When the question is about spatial relationships, use measurements rather than relying only on appearance. SAMSON supports measuring distances, angles, and dihedrals, and measurements can be saved with labels.
Before measuring, decide which geometric quantity answers your question. A distance, an angle, and a dihedral describe different relationships, so choosing the relevant one helps keep the check focused. Saving a measurement can also make the result easier to revisit as you continue working, instead of relying on memory or repeating the same check later.
4. Use history as part of safe experimentation
Undo and redo are not just emergency buttons. They let you explore a change, assess its result, and move backward or forward through document history. That can make trial-and-error work feel more manageable: you can test an edit, check what it changed, and recover if it was not useful.
For a clearer record of your own reasoning, consider making one intentional change at a time and checking the result before continuing. This is a practical habit rather than a special requirement: it helps connect an action to its outcome, and makes it easier to decide what you want to undo or repeat.
A compact pre-edit routine
- Identify: select the nodes relevant to your task.
- Verify: inspect their properties before making a change.
- Check: measure the geometry if your question is spatial.
- Recover: use document history if an experiment needs to be reversed or revisited.
This sequence is useful whenever you are moving from simply viewing a structure to actively working with it. For the full guide and links to related topics, see Work with structures.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.