Title/Axes
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Dialog Box: Title/Axes [Input menu]

The title may be any information, up to 80 characters. It is printed on most output.

For a molecule using cartesian coordinates, the a, b and c axes should in most cases be 1.0 and the interaxial angles alpha, beta and gamma should be 90.0. However, molecules with trigonal or hexagonal symmetry can use either Cartesian coordinates and Cartesian axes as just specified, or coordinates on hexagonal axes with a gamma angle of 120 degrees. The symmetry matrices are adjusted for either case depending on whether gamma is 90 or 120 degrees.

The angles should be consistent with the data for the crystal which is entered in the Symmetry and Input Atoms dialogs. In particular, for monoclinic crystals in the second setting (b-axis unique), beta (and not gamma) should be non-ninety. VIBRATZ requires a unique axes to be parallel to z, but this orientation should be attained by entering a rotation of 90 degrees on x in the Pre-Calculation Rotations dialog.

If a trigonal rhombohedral crystal is to use the primitive cell, the a, b and c axes must be equal and the three angles must be equal. You must also select a rhombohedral setting in the Symmetry option.

Lattice translations check boxes. These boxes are extremely important because they determine whether the calculation is to be for a crystal if all three boxes are checked; for a molecule if all three are unchecked, and for a polymer if either one (chain) or two (sheet) are checked.

The conversion from crystallographic to Cartesian coordinates is made by setting c parallel to z, and b in the y-z plane (a* parallel to x). If you use hexagonal axes for a molecule, that is gamma = 120 degrees, the orientation is the same as for a crystal - the a2 or b axis is parallel to y, so that a1 or a is not parallel to x.

The orientation of the reference Cartesian axes in the Atoms Graphics Window is x pointing directly out of the screen or paper, towards the observer; y horizontal to the observer's right; and z vertical.