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Reorienting xyz axes

Hi, I have a molecule oriented on the screen as I want. However, the xyz axes are pointing in an unconventional way: x(red) is pointing down on the screen, y(green) is pointing to the right on the screen, and z(blue) is pointing out of the screen.

How do I reorient the xyz axes so they are in the conventional orientation – x(red) to the right, y(green) up, and z(blue) out of the screen – but without changing orientation of the molecule?

Andrew DeYoung
Carnegie Mellon University

Maybe the following approach suffices:

  • re-orient the the scene: after loading the model in question, click once on the blue four point star in the GUI’s tool bar about navigation, then hoover over the canvas while the left mouse button is kept pressed. The main aim is to orient the coordinate system according to your preference. It will rotate coordinate system and molecule alike.

  • then, while keeping one of the Ctrl keys pressed, do the same (hoover with the mouse while keeping the left mouse button pressed), to translate the model up/down within the plane of display. This adjusts the relative distance between the model and the three axis displayed. No change of the orientation of the molecule relative to the three axes, no change of the absolute (x,y,z) coordinates in the .xyz eventually exported.