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Check that you've entered the crystal data correctly. As a quick guide, use the
Transform > List Bonds command to check bond distances. If you find atoms at
zero-distance from the central atom, you've certainly made a mistake! (perhaps
you entered too many atoms in the asymmetric unit).
You may also have a problem with your symmetry. If you entered a spacegroup symbol,
it might be that you need to use an origin offset, or to experiment with different
origin settings. You'll probably find the Spacegroups Assistant dialog useful here:
display the Edit Crystal window (Edit > Structure), then click the Browser button. You can
now explore different spacegroups settings, including unconventional ones (turn on
the "Show Unconventional Settings" checkbox) and different origin choices.
If your atomic coordinates are correct but you don't get the correct coordination
polyhedra displayed, check the bond specifications: you may need to increase
the bond lengths (or edit the atom sizes if you're using the "calculate from radii"
bond length mode) to encompass all the coordinating atoms.
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