26.2 Residue Rigid Bodies

The original GSAS program only offered vector rigid bodies, but GSAS-II also allows a seconf type of rigid bodies to be defined. This type is called a residue rigid body and they have several advantages. The name comes from macromolecular crystallography because the part of an amino acid that remains in a protein after peptide synthesis is called a residue in biochemistry. The residue rigid body implementation was initially for amino-acid residues for proteins, but has considerable utility for organic and organometallic materials as well. While the residue rigid body does not offer refineable translation parameters, it does allow for defining refineable torsion angle parameters.

The process for defining a residue rigid body is more straightforward than the fairly complex process of defining a vector rigid body. You will simply supply Cartesian coordinates (in Å) for the atoms in the rigid body. Should you wish to add torsional degrees of freedom, you do this by designating the pairs of atoms that have the bond between them. Of those two atoms, one is called the “torsion origin” and the other “the pivot.” The atoms bonded to the pivot atom (called the riding atoms) and the atoms bonded to those atoms, and so on, are the ones that will be rotated as the torsion angle is changed. However, GSAS-II does not include H (or D) atoms as riding atoms. If H atoms are part of the group of atoms attached via a torsion, their position should be generated in the phase’s Atoms tab using the “Edit Atoms”/“On selected atoms...”/“Calc H atoms” and the “Edit Atoms”/“Update H atoms” menu commands. A visual example of a torsion rotation is shown in Fig. 26.3. Here the C5 atom is the origin atom for the torsion and the C6 atom is the pivot, so that the riding atoms are O7 and O8. Since there are no H atoms attached to the phenyl ring, had the origin and pivot been switched, the ring would have rotate and the O atoms would stay in their original position. These two approaches are equivalent. Use of either definition for the torsion origin and riding atoms would result in a refinement with differing rigid body parameters, but the resulting crystallographic structures should be the same, within a fraction of the s.u. values.

26.2.1 Inputting a Residue RB to GSAS-II

To define a residue rigid body, select the “Rigid bodies” data tree entry and then click on the “Residue rigid bodies” tab and then use one of the commands in the “Edit Vector Body” menu. The menu command choices include:

“Import XYZ” This command will read Cartesian coordinates, for example from Avogadro or MolDraw, and will place the atoms into a residue rigid body.

“Extract from file” This opens a new tab labeled “Rigid body importer” where a multistep process is implemented for reading fractional coordinates and selecting atoms to be included.

1. Before attempting to use crystallographic coordinates to create a rigid body, confirm that the atoms you will want to use are all in the same asymmetric unit. You may need to reorganize which symmetry replicants are present and possibly even need to lower symmetry.
2. In the first step after you press on the “Extract from file” menu command, you identify a file to read from. This uses the phase importers (see §15.1.2 for more information on importers), so any of the formats that GSAS-II supports can be used.
3. Once the file is opened and read, you select the atoms that you want to use for creating the rigid body. The atoms in the asymmetric unit are displayed in the graphics window, with unselected atoms made much darker than selected atoms. Press “Continue” when you have selected the desired atoms.
4. The next window is shown as Fig. 26.4 and is quite sophisticated. The atoms that have been included from the previous step are now shown as a ball-and-stick model in the graphics window, where atoms are labeled with their number and element type. The upper two buttons on the left are used to select atoms, or selection can be done individually in the table.
5. The middle three buttons are used to align the origin and axes. This is discussed in more detail below in §26.3.1.0.
6. The there bottom buttons (which will create a vector body, a residue body or cancel the import) will complete this import operation and close the “Rigid body importer” tab. The “export as xyz” will write a file but does not close the tab. Note that only the selected atoms will be used. This means that atoms can be selected from structure file in step 3, that can be used for defining axes in step 5, but will not be included in the final rigid body if they are not selected in this step.

“Define torsion” This is used to add a torsion to a residue rigid body. You will be asked for the two atoms that define the bond. You can add as many torsion angles as is appropriate for your rigid body. The value of the angle torsion angle is an increment that is added to the initial torsion angle from the input Cartesian coordinates. The angle is measured clockwise looking from the rider atoms towards the torsion’s origin atom.

“Import residues” This command provides access to macros useful for working with proteins, but is unlikely to be used in any other context.

“Save/Read rigid body” The “Save rigid body” menu command writes the rigid body information to a file named with the extension .resbody and the “Read rigid body” will read them back. This is useful to duplicate a rigid body in a separate GSAS-II project.

When the residue rigid body is read into the GUI, the data window will appear as in Fig. 26.5. Here, torsions have also been defined. At this stage, only very minimal editing is possible. The orientation of the axes and the origin can be changed here by specifying three atoms for the “Orientation reference” settings, which are labeled as A, B and C. The first atom (A) will be set as the origin and the vector from the A atom to the second atom (B) will define the x-axis. The third atom (C) will define the y-axis so that the A, B and C atoms all lie in the x-y plane. The origin for the axes can optionally be changed using the “Center RB” button, which will set the origin to center of the rigid body (determined by averaging all coordinates without weighting for mass). The use of this will be demonstrated in §26.4.1. Note that if the “Orientation reference” settings are changed after use of the “Center RB” button, the origin is reset to the “A” atom.

The other controls on this window are: The name for the rigid body is set in the “Residue name” box. (It will be made unique if a name is repeated.) The “Plot” button displays the rigid body as a ball-and-stick diagram, where atoms are labeled by the atom name. The “Delete” buttton will delete this rigid body. The “Strip H-atoms” button is only present if the rigid body contains hydrogen atoms and will remove all H or D atoms from the body. The “H¡-¿D” button will replace all H atoms with D (\(\rm ^2H\)) or the reverse, if pressed again. The “Cycle XYZ” button permutes the x, y and z axes.