Editing a molecular structure can become frustrating when every change seems to create another decision: should you move the structure, build onto it, repeat it, or relax its geometry? A useful way to reduce that uncertainty is to separate those tasks and handle them in an order that matches your goal.
This workflow is for modelers who need to change a structure—not just inspect it. It helps distinguish basic repositioning from molecule construction, geometry refinement, and repeated arrangements, so you can focus on the operation that matters now instead of opening every tool at once.
Start by naming the job
Before editing, describe the immediate task in one sentence. For example: “I need to align this structure,” “I need to add atoms or fragments,” or “I need to make a repeated arrangement.” This small pause helps avoid a common detour: trying to solve a construction problem with movement tools, or reaching for geometry refinement before anything has been built.
- Changing position or alignment? Start with Moving objects. This is the foundational path for repositioning structures and learning about move editors and alignment tools.
- Constructing or modifying a molecule? Continue to Building molecules, which covers building with atoms, fragments, and the Asset Browser.
- Need to relax geometry? Read Minimizing when you are editing a structure and want to refine its geometry.
- Creating repeated arrangements? Use Creating patterns for linear, circular, or curved patterns.
Use the shortest path that fits
Not every project needs every step. If the task is simply to reposition or align a structure, the moving-objects workflow may be enough; you can leave minimization for another time. If you are not duplicating structures or building a repeated system, patterns are not part of your immediate path either.
For a molecule you are building and then refining, a sensible sequence is Moving objects → Building molecules → Minimizing. The first step gives you a way to position the structure, the next addresses construction, and the last addresses geometry after changes. Treat these as distinct stages: it is easier to understand what you are trying to accomplish when each stage has one clear purpose.
For a repeated system, first work through the relevant building steps, then use Creating patterns to make the arrangement. Minimization can follow when geometry refinement is part of the task. This route avoids treating pattern creation as a substitute for molecule construction: they address different parts of the workflow.
Choose the scope of geometry refinement
One useful decision is whether to minimize a whole molecule or only the part you are editing. The right scope depends on the task. If your changes are local, consider whether refining only the edited part is the more relevant choice; if the whole molecule needs attention, use the whole-molecule path. The documentation covers both options, so you can match the refinement scope to what you changed rather than assuming one choice fits every edit.
Keeping this decision until you know what you have built also makes the process easier to reason about. First identify and perform the structural change; then decide whether geometry refinement is needed and whether it should apply to the whole molecule or just the edited part.
A quick planning checklist
- Write down the immediate goal: reposition, build, refine, or repeat.
- Begin with the documentation page for that task instead of following every topic by default.
- Add the next step only when the project requires it—for example, construction before pattern creation.
- When refining geometry, choose between the whole molecule and the edited part based on the scope of the change.
This approach is useful for both new and experienced modelers: it gives newcomers a clear reading order and lets experienced users jump directly to the task at hand. For the complete overview and suggested paths, see the Build and edit documentation.
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