A defining feature of a crystallographic model is that it does not exist in isolation, but as part of a symmetric lattice. Crystal contacts (whether or not they are biologically relevant) are often important during refinement. ISOLDE's default visualisation mode represents crystallographically-related copies of the asymmetric unit as darker "ghosts" of the main model, updating with every coordinate change.

 

(Note: symmetry atoms cannot be directly manipulated, and do not currently take part in simulations. This is covered in more detail in the documentation.)