Adding Atoms from Crystal Mates

When you are working with a crystal structure (or any system that has periodic boundary conditions), you might want to examine atoms that are related to the displayed atoms by symmetry but are not actually displayed—that is, they are in a different copy of the asymmetric unit, biological unit, or unit cell. For example, you might want to examine interactions between a protein in the unit cell and the copy of the protein in the next unit cell. You can create structures in which neighboring atoms from adjacent replicas in the crystal are added. (This is done by performing the required symmetry operations on the crystal structure to generate a set of coordinates for these atoms.) These atoms are termed "crystal mates".

You can create and remove crystal mates by choosing an item under Edit → Crystal Mates. To do this, the Workspace must contain a single structure (entry), and the structure must have crystallographic information so that the symmetry operations can be applied to find the crystal mate atoms.

It's often useful to just add a layer of atoms around the existing structure. You can do this Edit → Crystal Mates and selecting a distance from the existing structure within which the symmetry-related atoms are added. To expand the structure in all directions with an entire copy of the structure, choose Edit → Crystal Mates → All Mates.

The new structure that is generated can be stored in a separate entry, or it can replace the existing entry. By default, the new structure is stored in a separate entry, and the new entry replaces the Workspace when it is created. The entry title is a copy of the title of the original structure with the distance value appended, and the entry is stored in an entry group named "title Crystal Mates". You can create multiple crystal mates with different distance values, and these are all stored in the entry group. As they are normal entries, you can delete an entry or the entire entry group. However, you cannot add crystal mates to these entries: instead you must use the original structure to create new crystal mate entries.

If you want the new structure to replace the existing entry, uncheck the option at Edit → Crystal Mates → Save as New Entry . If you replace the existing entry, you can restore it by choosing Edit → Crystal Mates → Remove All Mates.

The Materials Science profile has extra tools for crystal mates—see Workspace Tools for Periodic Structures.