The rotations in this dialog are those required to bring both the structure and the symmetry matrices (together) into proper orientation for symmetry analysis. This is required normally only for certain space groups (crystals). If you select the Space-Group Symmetry option, VIBRATZ usually detects such situations and supplies the appropriate rotations, but for space groups using the Custom Symmetry option it is necessary to enter the rotations manually.
VIBRATZ requires any unique axis to be the z-axis or crystallographic c-axis, whereas the standard orientation for monoclinic crystals is the unique axis is usually b, which is by default parallel to y. Thus monoclinic crystals in the standard second setting should be rotated 90 degrees on x.
Some trigonal, tetragonal and hexagonal space groups have either of two different orientations of the symmetry elements with respect to the axes. In some cases, only one of the orientations is consistent with the basis functions used for symmetry analysis used in VIBRATZ. Specifically, space groups in the point or factor group D2d, of the type P4m2 (where P and m may be replaced by other lattice and symmetry plane symbols respectively), must be rotated by 45 degrees. Space groups in the point or factor group D3h, of the type P62m, and of the point or factor group C3v of the type P3m1, must be rotated by 30 degrees. Space groups of the type P42m, P6m2 and P31m do not require rotation. See Orientation for more information about orientations and rotations.
Space groups in the point or factor groups D3 and D3d also may take two different orientations, but either orientation is valid without rotation. However, the Raman components which appear in the E species are different depending on the orientation.
Rotate lattice translation flags (polymers). If the lattice translation check boxes in the Title/Axes dialog refer to the original orientation of the axes entered in that dialog, if only some boxes are checked (i.e. the structure is a polymer and not a molecule or crystal) and if pre-calculation rotations are then applied, these indicators or flags may also need to be rotated appropriately. This is most likely with monoclinic space groups in which the unique axis is not c. For example if the unique axis is b and the polymer or lattice tranlation is c, then the 90 degree rotation on x would change the lattice translation direction to b or y. It is also possible to leave the Rotate lattice translation flags box in this dialog unchecked, and to select the lattice translation directions in the Title/Axes dialog as they are after the pre-calculation rotations. In the above example, this would mean checking the b-axis box as the polymer or translation direction.
Note that this option does not change the orientation of the atom coordinates relative to the symmetry matrices; rather it changes both of these, so that they are consistent with the Cartesian polynomial basis functions used for symmetry analysis. To rotate the input atom coordinates with respect to the symmetry elements, use the Rotate all atoms option in the Input Atoms dialog (Input menu).