Deleting Atoms and Atom Labels
Previous  Top  Next

In ATOMS normal operating mode, there are two types of atoms, input atoms and generated atoms. The input atoms are usually entered and removed in the the Input Atoms dialog. The symmetry and lattice translations, if present, are used to derive the generated atoms from the input atoms; it is the generated atoms which are actually viewed in a drawing. There are basically two ways of removing specific generated atoms from the drawing.

If only a few atoms are to be deleted, they can be marked as non-plotting. Clicking with the mouse on or near the location of an atom brings up either the Generated Atom Data dialog or the Atoms at Cursor dialog, in which selecting an atom brings up the first dialog. Unchecking the Plot Atom box will mark the atom as non-plotting. You must replot to actually cause the atom to be removed from the drawing. When the structure file is closed, a list is made of the non-plotting atoms, which will be saved and used the next time the structure is calculated. Starting with V4.0, the lists of deleted atoms and atom labels use a code containing the unit-cell, the symmetry operator etc., rather than an arbitrary generated-atom sequence number, so that changing the boundary conditions will not usually make the list invalid (although some deleted atoms or labels may no longer be within the boundaries). However, changing the symmetry will make the list invalid.

When molecules or fragments are present, the atoms in the entire group can be marked as plotting or non-plotting.

All atoms marked as non-plotting can be restored, and a specific range of generated atoms can be either restored or marked non-plotting, with the Atom/Bond Plot States dialog in the Input2 menu.

If many generated atoms are to be deleted, it may be better to change to the special Input=generated operating mode. This is done with the Generated to Input command in the Transform menu. In this operating mode, all symmetry and boundary conditions are removed, and generated atoms are exactly equivalent to input atoms. The individual atoms can be removed in the Input Atoms dialog. You can click on atoms on the screen and use the Generated Atom Data dialog to get the number, then delete them in the Input Atoms dialog. Or, you can mark atoms for deletion by unchecking the Plot atom box as above, then do the Generated to Input command. This command gives you an opportunity to delete atoms which are marked as non-plotting. It can be repeated as many times as necessary, just for the purpose of deleting atoms in this way.

Deleting angle labels. Angle labels are automatically applied to all groups meeting the specifications in the Angle Labels dialog (Display menu). Individual angles can be deleted (actually, marked as non-plotting) by clicking on the three atoms in succession (outer-central-outer) and unchecking the Angle box which appears in the Generated Atom Data dialog.