A small change to a molecular structure can be easy to make—and surprisingly hard to evaluate if you lose track of what you selected or what changed. Maybe you meant to inspect one residue but selected a larger part of the system. Maybe you adjusted a property and now want to compare the result with the previous state. These are ordinary moments in molecular modeling, and a simple workflow can make them easier to handle.
In SAMSON, working with a structure involves more than editing coordinates. You can select nodes, inspect or adjust their properties, measure geometric relationships, and use document history to move backward or forward through changes. Treating these as connected steps helps you work deliberately rather than relying on memory.
1. Make the selection your first checkpoint
Before inspecting or changing anything, confirm that you have selected the nodes you intend to work with. Depending on your task, those nodes might be atoms, residues, molecules, or other parts of the document. SAMSON supports selection through commands, editors, filters, or the Node Specification Language (NSL).
The useful habit is not to assume that a selection is correct just because you made it. Pause and check its scope before moving on. This is especially helpful when your next step could affect multiple nodes: a selection that is broader than intended can make a perfectly reasonable action produce an unexpected result.
If you are new to this workflow, start with the Selecting guide. It is the foundation for the inspection and measurement tasks that follow.
2. Inspect before you edit
Once the intended nodes are selected, inspect their properties. The Inspector is where you can check and adjust node properties, so it is a natural place to verify what you are working with before making a change. Separate two questions: “Is this the right node?” and “Is this the property I intend to change?” Answering both reduces the chance of making an edit based on a mistaken selection or assumption.
For a careful pass, note the property you want to review, check it on the selected nodes, and make only the adjustment you actually need. Then inspect the result again. This creates a clear before-and-after comparison without requiring you to remember several simultaneous changes.
The Inspecting guide covers checking and editing properties of selected nodes.
3. Measure when visual judgment is not enough
Structures are often viewed in three dimensions, where perspective can make spatial relationships difficult to judge by eye. If your question is geometric, use a measurement rather than relying only on how close or aligned features appear on screen. SAMSON’s measuring workflow covers distances, angles, and dihedrals, and measurements can be saved.
A measurement is most useful when it answers a specific question. Decide what relationship you need to check, select the relevant nodes, and create the corresponding measurement. Saving a measurement can also help keep that check available as you continue working, rather than turning it into a number you saw once and then have to reconstruct.
For details, see Measuring.
4. Use history as part of the workflow
Undo and redo are not just emergency buttons for obvious mistakes. They are useful when exploring a change and deciding whether it helped. If an edit does not produce the result you expected, document history lets you move backward and forward through document changes. That makes trial and error more manageable: you can test an adjustment, evaluate it, and recover a previous state when needed.
History works best alongside deliberate checkpoints. Keep the selection focused, make changes in a way you can evaluate, and use undo or redo when you need to revisit the sequence of changes. This is not a substitute for checking your work, but it gives you a way to navigate changes while you do.
See History: Undo and redo for more on moving through document history.
A practical sequence to remember
- Select: identify the nodes relevant to your task.
- Verify: check that the selection has the intended scope.
- Inspect: review the properties before adjusting them.
- Measure: use distances, angles, or dihedrals when geometry is the question.
- Review: evaluate the result and use document history if you need to move backward or forward.
This sequence is useful whether you are making a small property adjustment, checking a geometric relationship, or simply learning how a structure behaves as you explore it. It turns “I hope I changed the right thing” into a repeatable process: select carefully, inspect, measure when appropriate, and keep track of changes.
For the full overview and recommended paths, visit Work with structures.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.