Cutting structures inside/outside a sphere

Cutting outside a sphere

There are cases in which one would like to delete all atoms outside a sphere centered on given atom. With this option all atoms which are within the sphere radius will be kept. The case of quartz is shown below.

This is achieved by (Edit--->Delete atoms in  a region...) menu. Then click a button in the dialog bar (Sphere cut region--->Outside) and click the atom to which the sphere radius is defined. Move the mouse so that a sphere of variable radius is defined.

By clicking the right-button mouse all atoms outside the sphere will be deleted. The final results is shown in the fifth and sixth thumbnail below: the latter is the final structure rotated by 90 degree around the Y axis to show the spherical shape of the final structure. See how different is the result from cutting outside a circle.

Cutting inside a sphere

At variance with the previous case, sometimes one would like to delete all atoms inside a sphere centered on an atom. The procedure is the same as explained for the case above. Instead of pressing the button (Sphere cut region--->Outside) in the dialog box press the (Sphere cut region--->Inside). All atoms within the defined sphere will be removed. The pictures below show the last two steps in the procedure in which it is shown the missing zone in the last picture.

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