The process for using rigid bodies in a refinement is a two-step process. First, the rigid body must be defined, as has already been discussed in this chapter. The definition process is independent of any specific crystallographic information on how the body is used and indeed saving the rigid body to a file will allow your hard work to be “recycled” in a future project. The second step, which we call inserting the body into a structure, is where the rigid body is integrated into a crystal structure model. (This is what is shown in table in the Atoms tab.) Rigid bodies are added and changed using the “RB Models” tab for the phase and are inserted using the “Edit Body”/“Locate & Insert Rigid Body” menu command. Once a rigid body has been selected to insert into the structure, the data window shows information about the rigid body, as seen in Fig. 26.19 and the insertion process is started. In the insertion process, one defines:
This process for inserting a rigid body offers several mechanisms to change the position and orientation of the rigid body. One can type numbers into the GUI, or use the azimuth slider and see immediate changes in the graphics window. The mouse can also be used to change the position of the rigid body. Note that the following mouse actions are defined for the visualization of the structure (discussed in Chapter 18):
When the Alt key (Option key for MacOS) is held down while using the mouse, the mouse actions reposition the rigid body rather than change the view of the structure:
Note that with Mac and a single button mouse, it is possible to hold down control+option and use the mouse drag to simulate the right mouse button drag or use command+option to simulate the middle mouse button drag. I recommend getting a three-button mouse, instead.
The other mechanism for repositioning a rigid body involves specifying pairs of atoms between the rigid body and the structure. The rigid body can be translated and/or oriented so that the specific atoms are moved as close as is possible. This is done with the lower section of the data window, as seen in Fig. 26.20. This part of the window is also used to determine how atoms in the rigid body are mapped to atoms in the structure. I will call the table of atoms shown here as the “Assignments Table.” Note that the first two columns of the table show the rigid body label and the atom type. The third, fourth and fifth columns show the atom in the structure that is paired to the rigid body atom, as an atom number, atom label and the distance between the paired atoms. By default, atoms are paired by shortest distances. Note that as the rigid body is moved, these distances are updated and pairing assignments are revised if the closest atoms change. The last column allows one to override this pairing by assigning a specific atom in the structure to be paired to the rigid body atom. These assignments are also used for the “Set Origin,” “Set Orientation,” and “Set both” buttons, which will be explained in a subsequent paragraph. Optionally, use the “Update Assignments” button to the right of the assignments table, after making an assignment to update the list of paired atoms and their distances.
When the rigid body import process is completed using the “Add” button (immediately above the table), the rigid body atom will be added to the phase with the position, orientation, and any torsion angle(s) that has been specified. Each atom in the rigid body will be linked to an atom in the structure where the coordinates, occupancy, and \(\rm U_{iso}\) or \(\rm U_{\it ij}\) values in the Atoms table will be updated to match what is generated from the rigid body. Note that one option for the atom assignments is “Create new,” which is used to indicate that a new atom atom should be added to the structure to pair to the rigid body rather than use an atom that is already defined.
When atom pairs are assigned manually, the “Set Origin,” “Set Orientation,” and “Set both” buttons to the right of the table can be used to set the rigid body location and orientation. At least one atom must be selected for “Set Origin” to function. This will set the Origin fractional coordinates to minimize the distance(s) to the paired atom(s). If two or more atom pairs are assigned manually, the “Set Orientation” button can be used. This sets the Orientation azimuth and Orientation vector values to minimize distances. With three or more atoms assigned, the “Set both” button will set the Orientation azimuth and vector as well as the origin coordinates. The use of these will be illustrated later (in §26.8).
One potentially tricky aspect of assigning atom pairs manually is determining which atoms should be paired. This can be aided by highlighting atoms in the graphics window. If you select a row in this lower section of the data window by clicking on the rigid body label, that atom in the rigid body is highlighted by changing its color to green. Likewise, the paired atom in the structure is also highlighted by changing that atom’s color to green. Should you wish to find a different atom in the structure, the “Crystal Highlight” selection to the right of the assignments table can be used to select an atom to highlight.
Once the body has been inserted, a window such as what is seen in Fig, 26.21. Note that this window shows the location of the rigid body origin in fractional coordinates, the azimuthal angle and a unit vector in fractional coordinates that position and orient the body. There are refinement flags for the origin and orientation. The refinement modes for orientation refinement (A, V, and AV, which are explained in the next section.) This window allows the overall fractional occupancy for the rigid body to be refined. As noted before, if the Alt key is held down (the Option key for MacOS), the rigid body is moved or rotated rather than changing the view of the entire model.
There are a number of ways that the ADPs for rigid bodies can be fit. The default is where all atoms are assigned the same \(\rm U_{iso}\) value but Translation-Libration-Screw (TLS) group motion descriptions (see §26.9) are also offered.
