CrystalMaker Online Help

CrystalMaker Guide:

Working with Molecular Crystals

What are Molecular Crystals?

Molecular crystals are crystal structures which contain discrete bonded units ("molecules") with no long range bonding between the units (in reality, weak Van der Waals or hydrogen bonds may exist to hold the molecular units in place - but these weak bonds are rarely displayed). Examples of molecular crystals include the structures of organic molecules, and some inorganic compounds such as sulphur hexafluoride (SF6). Examples of non-molecular crystals (i.e., with strong, long-range bonding) include most minerals (e.g., quartz, feldspar, garnet), ceramics, oxides, and so on.

Problems working with Molecular Crystals

Generally one 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. Isolating a single molecule is possible using the selection tools - but for complex structures, this can be time-consuming. In the following note, we describe ways to make your life easier...

1. Displaying Only Intact Molecules

The Transform > Hide Molecular Fragments command will search through the bonding specifications and hide any molecules which are incomplete. This command is ideal for viewing the ways in which molecules pack together.

Please note, for this command to be effective, you should ensure that you have first specified a sufficiently-wide range of fractional coordinates (using the Transform > Set Range command), so that several molecules fit within the display range. (If your range of coordinates is too small, then there's the danger that no intact molecules exist within this range, and the Hide Molecular Fragments command will hide everything!).

2. Isolating a Single Molecule

If you wish to display only one molecule, with the rest of the crystal structure hidden (and you're sure that that is an intact molecule), perform the following steps:-

Select the Arrow tool from the toolbar
If you already have selected atoms in your structure, deselect them (clicking on a blank portion of the graphics window will do this)
With the Arrow Tool active, click on an atom in the molecule you wish to isolate. The atom should be shown as selected (with a yellow or red halo).
Select the Selection > Hide Other Molecules menu command. The structure will be replotted with most of the atoms hidden - the only atoms shown are those that are bonded directly, or indirectly, to your selected atom.

If you wish to isolate several molecules, you just need to select one or more atoms in each molecule, then execute the Hide Other Molecules command.

Please note: as for the Hide Molecular Fragments command, the Hide Other Molecules command only works for molecular crystals. You should also ensure that the molecule you select is fully bonded. It might be prudent to use the Hide Molecular Fragments command first - to show intact molecules, and then to go one stage further and select an atom in one molecule and use the Hide Other Molecules command.

3. Selecting an Entire Molecule

If you want to highlight a particular molecule, you should first select one atom in that molecule, and then use the Selection > Select Entire Molecule menu command. All other atoms in the molecule will then be marked as selected. This lets you move the molecule as a single unit (but clicking on a selected atom with the Arrow Tool, and then dragging the molecule) - and might be useful if you've "placed"a molecule into another structure (e.g., to visualize how the molecule might fit onto a crystal surface).

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