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

Wrap On Move (PBC)

By default, translations do not wrap atoms back into the unit cell. To enable PBC wrapping after moving atoms, set wrapOnMove to true (a valid cell and pbc flags are required).

editor.avr.wrapOnMove = true;

You can also toggle this in the GUI under Boundary.

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, two, or three atoms, then press a again to exit axis picking. One atom sets the rotation center (camera axis), two atoms define the bond axis, and three atoms define the plane normal through their centroid. If exactly three atoms are selected, the rotation axis is the normal of the plane through those atoms, centered at their centroid. 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