Crystal cell edit

MOLDRAW allows to define and edit the crystal cell parameters by means of the

(Crystal-->Edit cell parameters...) menu. The following widget appears:

The widget allows to manually change the a, b, c, alpha, beta and gamma cell parameters.   Cell edges a, b and c can be multiplied by an user selected scale factor, to easily expand or compress the cell volume. This option is very useful to defines supercells, i.e. multiples of the original cell.   Cell angles can set directly or by clicking three non-colinear atoms.   The cell itself can be moved in the X-Y plane by any amount. Standard shifts are also provided.   The view can be set perpendicular to any to any (h k l) crystallographic plane or to any [u v w] direction.   The cell axis reference can be maintained exactly as the original one or redefined by considering the a cell edge to lye along the MOLDRAW X-axis.

Defining a new crystal starting from a molecule

Let us start from a simple water molecule as displayed here after selecting the (Crystal-->View cell borders) menu.   Because we are dealing with a molecule the unit cell is a cube with edge equal to 1.

If we now want to generate a crystal in which a unit cell contains just one water molecule separated by enough room from its neighbours in the adjacent cells, we can proceed by invoking the (Crystal-->Edit cell parameters...) menu.   By clicking the x2 buttons a new cell with a=4, b=4 and c=4 is generated. Now click the Apply button to proceed.

Open the (File-->Save MOL file-->Fractional XYZ) menu and save the file with the name test_cell.mol. Answer NO when a dialog asks if only the atoms in the unit cell should be saved. Read the new file back by clicking the Read label on the toolbar. Then click the Pack label on the toolbar and by sliding the dialogs a unit cell as shown here should be generated.

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