Locate Groups
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Dialog Box - called from: Transform Menu

This allows you to isolate individual molecules, polymers or other structural groups in a crystal. You must specify a single "seed" atom, then all other atoms interconnected to this one are located. The interconnection is by bonds specified in the Bonds input, or polyhedra specified in the Polyhedra input in the Input1 menu. There must be no bonds (except those marked inter-molecular) from atoms in a group to atoms outside the group, nor can polyhedra connect atoms within and without the group.

If the structure consists of discrete molecules, not polymers, it is usually easier to use one of the Molecules in Crystal Boundary options. These will automatically identify any and all molecules. See Dealing with Molecules, Groups and Fragments for more information on strategy for dealing with groups. Note also that ATOMS V5.1 differs from previous versions in the way groups are identified - several groups can be identified and this identification persists regardless of whether the atoms are marked for non-plotting or not; and groups may be directly converted to fragments with the Generated to Input option (Transform menu).

Creation of a structure file for displaying such groups involves three steps. Note that the Find button in the Generated Atom Data dialog (which appears when you click on an atom) is an alternative to step 2 (that is, to this dialog).

1) Setting the original boundary option. Before exercising the Locate Groups option, the molecules or other groups must be within the boundaries of a structure calculated in the usual way. For example, you can use the Default Unit Cell option, suboption -1 to 1; this gives one full unit cell on either side of the origin (for a total of 8 unit cells).

2) Locating the group(s). To do the actual isolation of the group, call on this dialog - Locate Groups or use the Find button in the Generated Atom Data dialog. You must specify an initial or "seed" atom; this can either be a specific generated atom, or an input atom. If you use a generated atom, it will normally be necessary beforehand to use the on-screen atom-location feature (see Generated Atom Data ) or a print-out from the List Generated Atoms command in the File menu to find the number of a suitable atom. Actually, when using a generated atom the Find button in the Generated Atom Data dialog is usually more convenient than using this dialog (Locate Groups). However, this dialog is the only way to use an input atom (see the list in the Input Atoms dialog in the Input1 menu, or the List Input dialog in the File menu). In this case, ATOMS will test all the generated atoms in the equivalent set derived from that input atom, and find the one which is closest to the origin.

When you click on OK, ATOMS makes a temporary list of all atoms in each group.

3) Saving the Structure. After you are finished with step 2, you are presented with the Groups Located dialog, which allows a) restoration of the non-plotting atoms, which will not undo the process of group location (as in pre-V5.1 ATOMS); b) locating an additional group; or c) converting the generated atoms to input atoms. If you leave the dialog without doing any of these things, the molecule(s) can be highlighted or hidden in various ways.

You may wish to turn on centering with the Centering/Displacement dialog in the Input2 menu if the group(s) are not near the origin.

The "deletion" of atoms (see Deleting Atoms) or marking for non-plotting, does not directly affect the location of groups. That is, if you mark an atom for non-plotting, neither the atom nor bonds to it are shown in the drawing, but the atom and its bonds still exist for the purpose of locating groups. In order to remove atoms and bonds permanently before locating groups, you must convert Generated to Input (Transform menu), selecting the option to remove non-plotting atoms. Or you can convert Generated to Input and then delete the atoms. Then recalculate to reestablish bonds and polyhedra, and proceed with location of groups.