Edit

Selection

  • Click an atom to select it. Click again to deselect.

  • Shift + drag to box-select multiple atoms (selection accumulates).

  • Shift + Alt + drag to lasso-select multiple atoms (selection accumulates).

Advanced Selection

Draw a mesh primitive and select atoms inside it.

Group-based Selection

Tag atoms into named groups and select them later by group name. Each atom can belong to multiple groups.

Example (JS):

// add selected atoms to a group
editor.ops.atoms.AddAtomsToGroupOperation({ group: "molecule" });
// remove selected atoms from a group
editor.ops.atoms.RemoveAtomsFromGroupOperation({ group: "molecule" });
// clear a group from all atoms
editor.ops.atoms.ClearGroupOperation({ group: "molecule" });
// select atoms by group
editor.ops.selection.SelectByGroup({ group: "molecule" });

You can also manage groups directly on the Atoms object:

atoms.addAtomsToGroup([0, 1, 2], "surface");
const indices = atoms.getGroupIndices("surface");

Move, Rotate, Scale

Select atoms and use keyboard shortcuts to transform them, then move the mouse to apply the transform and click to confirm.

  • g translate

  • r rotate

  • s scale

Rotation defaults to the camera axis through the selection center. To rotate around a custom axis, press r to enter rotate mode, then press a and click one or two atoms, then press a again to exit axis picking. One atom sets the rotation center (camera axis), two atoms define the bond axis. The axis is shown with orange crosses and a long orange line (for two atoms), and stays active until you redefine it. Press a again to exit axis picking and rotate; click an axis atom again to deselect it. Press r then x, y, or z to lock rotation to a world axis (press the same key again to unlock).

Translate Axis Lock

Press g to translate, then press x, y, or z to lock movement to that axis. To translate along an atom-defined axis, press g then a and click two atoms, then press a again to exit axis picking. To translate in an atom-defined plane, press g then a and click three atoms, press a again to exit axis picking, then press p for plane or n for normal.

  • g, move

  • r, rotate

  • d, copy and move

  • Delete or x, delete the selected atoms