If your structure seems to have too many atoms in the unit cell, this could be because the symmetry has not been correctly set, or perhaps your structure is disordered.

1. Incorrect spacegroup and/or origin setting
   Your first task should be to ensure that the symmetry has been entered correctly. Usually this will be in the form of a spacegroup symbol that CrystalMaker can interpret (e.g., "F d -3 m"). Note that some spacegroup symbols are ambiguous, because they don't uniquely specify an origin choice. In these cases you may just need to check whether origin setting 1 or 2 is to be used.

   To change the origin setting for a spacegroup it's generally easiest to use the Spacegroups Browser: choose the Edit > Structure command to display the Crystal Editor window, then click the Browse button to the right of the Spacegroup field. You can display all conventional (and unconventional) settings, and you should see that some spacegroups are listed with multiple origin settings.

   If your structure has been loaded from a text file (e.g., a CIF file), then chances are that CrystalMaker will have used the general equivalent positions listed in the file. These are unambiguous, and are much safer to use than relying on a text string to specify the spacegroup symbol.

2. Duplicate Atoms
   Sometimes a structure is specified with too many sites. This could be because the atom list contains more atoms than is needed (for the asymmetric unit), or because there is no other way to specify the presence of different element types disordered over the same positions in the unit cell.

   • Redundant Atoms. Some authors erroneously include too much data for a crystal structure, listing the full contents of the unit cell, in lieu of the asymmetric unit. If the full unit cell is entered, together with a higher-symmetry spacegroup, the result is that duplicate atoms may be generated.

   • Substitutional Disorder Another way in which duplicate sites may be generated is if authors have entered the same site coordinates for different elements, in an attempt to specify chemical disorder (e.g., Al/Si disorder in silicate structures). This is a rather clumsy approach: CrystalMaker lets you enter multiple elements for the same site (e.g., "Al 0.4 Si 0.6"), and the program tries to consolidate same-site data when loading files from other formats.

   CrystalMaker will normally warn you about duplicate sites, but it might be an issue if you are importing data from a text file. In this case, the best option is simply to identify which sites are duplicate (you can use the Site Browser's Vis checkboxes to turn sites on or off), then delete them using the Edit > Structure command, or by selecting one site and pressing the Delete key on your keyboard.

3. Split Sites
   Many structures are refined with so-called "split sites". Here, two or more closely-separated (or even overlapping) atoms are used to represent a single site.

   Now, the real structure doesn't have multiple atoms on top of each other - but it probably has some kind of positional disorder. This could be static (e.g., some atoms are off-centred to the left, whilst others are off-centred to the right - as in some ferroelectric materials such as barium titanate), or dynamical - where lattice vibrations mean that an atom's precise position can't be easily defined and instead, several "dummy atoms" are used to indicate a range of positions.

   You may wish to merge the split sites back together (as described below), or alternatively, you might opt to hide some of the sites - using the Site Browser's Vis checkboxes, or by selecting certain atoms and choosing Selection > Hide > Selection.

Merging Split Sites

Let's assume that you've verified that all your input data are correct, including the symmetry, and that your structure shows genuine disorder. You have split sites, possibly with overlapping atoms, and you want to somehow replot the structure showing a more idealized representation.

You can "merge" the split sites back together by replacing them with a single site. You can calculate the ideal coordinates for this single site by selecting all the relevant atoms, then calculating their mean coordinates - in other words, their centroid. This is possible using the Selection > Calculate Centroid command. The result is printed in the Log pane of the Overview window.