Align Face or Vector
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Dialog Box - called from: Rotation Menu

This will rotate a specified face (hkl) to lie flat in the screen or paper (face-normal parallel to x observer), or a vector (uvw) to be perpendicular to the screen or paper. To align a face, it is also necessary to specify a vector lying in the face which will be vertical in the screen or paper (z direction). Conversely, to align a vector, it is necessary to specify a face, containing the vector, whose normal will be vertical. If a vector [uvw] lies in a face (hkl), the indices satisfy the condition hu + kv + lw = 0. If clinographic viewing is in effect, it is turned off when the face is aligned, to simplify any subsequent rotations.

You can elect to use the default alignment vector or face, instead of specifying it. The default vector will be the intersection of the face (hkl) with the face (100), whose indices are given by the cross product (hkl)x(100). If the face (hkl) is (100), the default alignment vector will be the vector [001]. For aligning a vector the algebra is just the same, with interchange of face and vector.

When dealing with a molecule or polymer, using a Cartesian axial system, this rotation option can be used to obtain a view down a given vector direction. Use the vector alignment option, although when the structure axes are Cartesian the two cases of aligning a face or a vector are identical. After specifying the initial vector or view direction, if you do not accept the default you must then give another vector, in place of the "face indices", which is perpendicular to the first vector, and which is to be vertical (z direction). If the two vectors are at right angles, their coefficients or "indices" multiplied together (the vector dot product) should equal zero as in the above condition for a vector lying in a face.

Coordinate system (Input=Generated). When in the special Input=Generated boundary mode, you can choose to align the structure (and the aggregate if more than one structure fragment is present on either the original crystal axes (if the structure was originally a crystal), or the Cartesian axes to which the atoms were transformed when the last Generated to Input operation (Transform menu) was performed. Note that before V6.3 the alignment was always done on the Cartesian axes of the structure - if you want to continue with this behavior, select Cartesian axes.