Build a Structure

Create a molecular or periodic starting structure with a method appropriate to the scientific question and preserve enough provenance to reproduce it.

Before you begin

Choose the least ambiguous source:

Use a crystallographic or otherwise defensible source when numerical conclusions depend on the geometry.

Procedure

1. Open Library and search by name, formula, or tag when an appropriate entry exists.
2. For a molecule described by connectivity, open the Add panel in SMILES mode, enter the string, and inspect the preview before placement.
3. For a small edit, use Add Atom and the transform tools, then measure suspicious bonds.
4. For generated families, create the structure in reference/run.js with tako.structure.Atoms, bulk, crystal, repeat, or other documented helpers.
5. Save the starting structure under input/ or record the external source identifier.
6. Optimize before interpreting single-point properties unless the fixed geometry itself is the question.

Verify the result

Check formula, charge, multiplicity, atom count, bond connectivity, closest contacts, periodic cell, and intended dimensionality. For a generated series, verify that only the intended parameter changes between members.

Variants

• Build fragments separately and keep them in layers before merging.
• Generate several orientations or conformers in a script rather than relying on one manually chosen pose.
• Use fractional coordinates for periodic structures only when the cell and convention are explicit.

Troubleshooting