When working with molecular crystals, one generally wishes to visualize either individual molecules, or the way in which intact molecules mesh together to build a cohesive crystal structure.

Unfortunately, an individual molecule may extend beyond a single unit cell, and it can be quite difficult to adjust the range of coordinates so that intact molecules are shown: nearly always one gets fragments of other molecules appearing, and this can make the overall structure look very complex. The Transform menu has a dedicated Optimize Range submenu, with commands designed to address this problem.

Displaying an Optimum Unit Cell View

The Show Molecular Cell command calculates the best arrangement of (fully-intact) molecules to be displayed, corresponding to a complete unit cell's contents. This command is a great starting point for working with a molecular crystal: you get the complete unit cell contents - and they are all intact molecules!

(Note that, in order to ensure that all molecules are intact, some atoms may straddle the unit cell boundary; other atoms that lie within the unit cell may be hidden, to ensure that only one unit cell's worth of crystal is shown.)

Repairing Molecular Fragments

If you have chosen an arbitrary view of part of a crystal, (e.g., by using the Set Range command), some of your molecules may well have been truncated - this happens when they straddle the plot range. You can "repair" these molecular fragments with the Repair Molecular Fragments command: the program generates additional atoms so that all atoms in the original view are now part of intact molecules.

Hiding Molecular Fragments

An alternative to repairing molecular fragments is simply to hide them. The Hide Molecular Fragments command searches through the bonding specifications and hides any molecules which are incomplete. This is good when you are working with an extended plot range (i.e., several unit cells), and wish to tidy up your display so that you can see the proverbial wood for the trees.

(If you just want to show one or more molecules associated with a single unit cell, use the Show Molecular Cell command instead.)