Dialog Box - called from: Transform Menu
Multiple structures fragments can be used to model twinning, epitaxy and certain types of crystalline defects, as well as interactions between molecules. Each structure can be rotated and translated independently; however, there is only one list of bonds and of polyhedra, and both are located throughout the structure as a whole.
Thermal ellipsoids for multiple structures are not supported; temperature factor information is lost if you introduce multiple fragments.
Most operations on individual structures are carried out through this dialog in the File menu. However, individual structure fragments can be rotated and translated in some simple ways using the Dialog Bar - Fragments (Display menu).
Before more than one structure can be dealt with, each of the structures concerned must be transformed to the "Input=generated" mode with the Generated to Input command in the Transform menu.
The Multiple Structures dialog gives a list of the current structure fragments. The first fragment is always the main structure. There are two ways to add additional fragments; the Duplicate button and the Read File button.
If you choose Duplicate, the new fragment will have the same orientation and center point as the current fragment. You have the option of inverting the current fragment, that is, negating all the atomic coordinates. All the types of the atoms remain the same, and the lists of bonds and polyhedra are not duplicated. The title is copied to the new fragment (the title for fragment number 1 is that of the structure as a whole).
The Read File button calls up the Read Structure Fragment from File dialog. The Revise button calls up the Revise Structure Fragment dialog.
After duplicating a structure or reading in an additional structure fragment, you must choose Calculate from the File menu in order to locate bonds and polyhedra. The Calculation Output dialog in the Input2 menu allows you to get a listing of only those bonds and bond angles which involve more than one fragment, i.e. inter-fragment bonds. To get such a list you must have some sort of calculation output turned on, and the bond distances and/or angles print-outs turned on also.
You can highlight, dim or omit interfragment bonds with a Combo box in either the Dialog Bar - Right or the Atom/Bond Plot States dialog (Input2 menu). Individual fragments can be rotated or moved with DialogBar - Fragments.
Note that clicking with the mouse on an atom in the drawing on-screen brings up the Generated Atom Data dialog, which lists the bond distance to the last atom, and the bond angle involving the last three atoms.