Atoms
| # | El. | x | y | z |
|---|
1. Origin
Moves the centroid of the selected atoms — or of all atoms, if none are selected — to (0, 0, 0).
2. Align to axes
Assign one or more selected atoms to an X, Y and/or Z group — like -x 2 -y 3 -z 4 — then run.
Any combination works (X only, X+Y, or X+Y+Z); atoms already used for the origin can be reused here.
X
Y
Z
3. Rotate (°)
Rotation about the x-, y- and z-axis, applied in that order (matches -r x y z).
4. Translate (Å)
5. Custom rotation matrix
3×3 matrix applied directly to the coordinates (matches -m x1 y1 z1 x2 y2 z2 x3 y3 z3), e.g. -1 0 0 / 0 -1 0 / 0 0 -1 to invert.