Cutting structures outside/inside a circle

Cutting outside a circle

There are cases in which one would like to delete all atoms outside a circle defined in the X-Y plane. With this option all atoms which are within the circle will be conserved irrespective of their Z value. 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 (Circle cut region--->Outside) and click a point in space (in this case close to the center of masses). Move the mouse so that a circle of variable radius is defined. By clicking the right-button mouse all atoms outside the circle 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 that all atoms within the defined circle are still present, irrespective of their Z-coordinate. 

Cutting inside a circle

At variance with the previous case, sometimes one would like to delete all atoms inside a circle defined in the X-Y plane. The procedure is the same as explained for the case above. Instead of pressing the button (Circle cut region--->Outside) in the dialog box press the (Circle cut region--->Inside). All atoms within the defined circle will be removed, irrespective of their Z-coordinate. The pictures below show the last two steps in the procedure in which the last picture highlights the circular "hole" left in the structure.

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