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 > Atom Range submenu has commands to help here.
It is crucial that you check your bond specifications, before proceding to use one of the Optimize Range commands, otherwise you may find "incomplete" molecules are displayed.
A common mistake is to use the wrong Element Table at the outset, so that bond specifications use inappropriate atomic radii, with the result that not all bond linkages are created. This is especially a problem if you tend to use organic structures. CrystalMaker's default element table is set up for inorganic structures, and you may find that C-C and other common bond distances are too small.
If this is the case, please use the Elements pane of the Preferences window, and choose a more appropriate element table (e.g., the CSD CrystalMaker Covalent Radii), which you can then apply to an existing structure (remembering to edit your bond specifications afterwards) and Save as your default set for later use.
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.)
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.
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.
For the Hide Molecular Fragments command to be effective, you should first ensure that you have specified a sufficiently-wide range of atoms (e.g., using the Set Range command) so that at least one intact molecule fits within the display range - otherwise there's the danger that everything may get hidden!
(If you just want to show one or more molecules associated with a single unit cell, use the Show Molecular Cell command instead.)
See Also