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Generating Clusters

CrystalExplorer provides several methods for building up clusters of atoms or molecules.

Complete Fragments

Many options in CrystalExplorer can produce 'incomplete' molecular fragments.

Indeed, a cif file may contain only an incomplete asymmetric molecular fragment.

By clicking on the fragment completion button in the main toolbar all bonded atoms in a fragment or molecule are generated, and only whole molecules are displayed.

Generate Unit Cells

This button generates multiple copies of the unit cell including any surfaces which you have made within.

A dialog box allows the user to choose the number of copies and direction in which to make the unit cell copies.

This is especially useful when combined with crystal void surfaces to show empty pores and channels in the structure.

Show/Hide Contact Atoms

By clicking on theShow/Hide contact atoms button CrystalExplorer shows ghost atoms.

These ghosts representing atoms close to the real atoms shown in the graphics window. By left-clicking on the ghosts, they become real atoms, and a new set of close-contact atoms is displayed. By repeated clicking on the ghost atoms, the connectivity of the crystal structure can be explored.

In this way, the cluster of atoms representing the crystal structure can be expanded.

The ghost atoms are turned off by clicking the Show/Hide contact atoms button again.

Generate Atoms Within Radius

This feature allows the user to generate a cluster of atoms within a specified distance of any atom currently selected.

When the button is clicked, a popup window appears; simply enter the desired distance.