Dialog Box: Generated Atom Data [click on atom in Atoms Window]
This gives information on the currently selected atom, in the currently selected mode.
The first line gives the generated atom number, as in the Final Atom List in the output, the label and the input atom number, as in the Input Atoms dialog (Input menu). In the case of a crystal or polymer, the atom is identified as either a primary or secondary atom.
Three sets of atomic coordinates are given; the current Cartesian coordinates, which include any rotations applied in the Atoms Window; the Original coordinates, which are the Cartesian coordinate in standard orientation (including rotations specified in the Pre-Calculation Rotations dialog, Input menu, and displacements to put the center of gravity on the zero point), and for a crystal or polymer, the fractional coordinates on the structure axes, in original orientation.
The motion vector is always Cartesian and is given in both the current orientation and the standard orientation as above. See the Basic Parameters dialog (Setting menu) for factors affecting the magnitude of the vectors.
The four lines at the bottom of the dialog give the distance from the current atom to the last atom selected, the angle defined by the current atom and the last two, the tau dihedral angle involving the last four atoms, and the bond-plane psi angle involving the last four atoms. See Construct Molecule from Z-Matrix for the definition of the dihedral angle and the sign convention. For psi angles, the sequence is 1) outer atom defining the "bond" of the bond-plane; 2) central atom; and 3) and 4) outer atoms defining the plane (see the diagram in Psi Angles or Manual Psi.
The buttons to the right of each of the lines for bond, angle, tau and psi allow specification of individual bonds and angles "manually", instead of "automatically" as in the dialogs in the Forces menu. Clicking on these buttons you will be shown respectively the Add Atoms to Manual Bond / Angle / Tau / Psi dialogs, which in turn lead to the Manual Bonds, Manual Angles, Manual Tau or Manual Psi dialogs. If the atoms specified are either in a pre-existing Manual Bond or angle, or have been generated with "automatic" bond or angle specifications, you will be given a warning, but will not be prevented from adding the atoms.