Coordination of Atoms
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Dialog Box: Coordination of Atoms [Input Atoms dialog, Input menu]

This dialog sets parameters for a print-out of interatomic bond distances and angles. The results are presented in two ways; 1) all bonds and angles involving the selected input atom, or each input atom in turn; and 2) lists of all bonds and angles, sorted according to bond lengths.

The results are written to a file name BONDS.VBD, and they also appear in a Text window (see Operation - Windows, Menus). This window has its own menu bar, which is different from the standard VIBRATZ menu bar. The Text window menu bar has standard commands for editing and printing out text. In order to access dialogs in the VIBRATZ menu bar, click on the Control window or select the Control window in the View or Windows menus.

If you check the All atoms radio button, each input atom will be analyzed in turn; if you check the Selected atom only button, results will be given only for the input atom previously selected in Input Atoms dialog - return to that dialog with the Cancel button.

The Distance limit - central-ligand applies to all bonds from the current input atom to surrounding atoms.

The Distance limit - ligand-ligand applies to the distances between the atoms surrounding the current input atom. This is normally the way that undesired angles are screeened out. For example for octahedral coordination around a central atom, only the ~90 degree angles involving adjacent ligands are usually selected, not the ~180 degree angles involving opposite ligands. This is done by setting this distance limit to just larger than the maximum ligand-ligand distance.

The Distance limit for angles (which also applies to ligand-ligand distances), is a test which is applied to the central-ligand distance of both legs of an angle. This allows consideration of next-nearest neighbors for bonds, but not for angles.

If the Do angles and ligand-ligand distances box is not checked, only central-ligand bond distances will be calculated.

When the structure is complex and all input atoms are computed at once, the Use radii to screen sorted lists allows exclusion of chemically unrealistic bonds and angles. If this is used, the overall distance limits above should be large enough for all interatomic distances. This option requires suitable atomic radii to be present in the Atom Types list (Input menu). The calculated bond lengths will be compared with the sum of the atomic radii, multiplied by the factor in the Factor for sum of radii box. A factor of about 1.2-1.3 is usually appropriate. The default radii, obtained from the ELEMENTS.DAT file (see Types of Files) are standard covalent radii, with some adjustments.

Note that values for individual bonds and angles can be obtained in the Atoms window by clicking successively on the atoms involved.