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Build Mode

Build Mode turns Atomiverse into a molecular editor. The loaded structure becomes an editable canvas — you can add atoms, insert fragments, adjust bonds and angles, and run a geometry relaxation when you are done.

Typical Flow​

  1. Start from an existing structure or from scratch.
  2. Pick an element from the periodic table in the left panel.
  3. Click an existing atom to replace its element, or click empty space to place a new atom.
  4. Use geometry adjustment to fix bond lengths, angles, or torsions.
  5. Click Optimize to relax the whole structure before moving into Run Mode.

What's in the Left Panel​

  • Periodic table — pick the element you want to add. It stays active until you change it.
  • Fragment library — insert common functional groups or ring systems in one click, or type a custom SMILES string to insert any fragment.
  • Geometry editor — appears when 2, 3, or 4 atoms are selected. Edit the corresponding distance, angle, or dihedral directly.

Where Build Mode Helps Most​

  • Assembling a scaffold from scratch
  • Quickly inserting a substituent or functional group
  • Correcting a bond length or torsion before a calculation
  • Patching up a structure imported from another tool
tip

Start simple and relax early. Adding a few atoms and then optimizing gives you a better starting point than building a large structure without any relaxation.