Dealing with Molecules, Groups and Fragments in Crystals
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Atoms has capabilities to deal with several types of atomic groups, which may be roughly separated into three classes.

1) True Molecules

It is often useful to be able to identify true molecules in crystals. A "true" molecule has strong bonds linking all atoms within it, does not have strong bonds linking its atoms to other molecules or groups, and is limited to a constant number of atoms, i.e. it is not a polymer.

True molecules which are not to be combined with other structures are most easily dealt with initially using one of the special Molecules in Crystals Boundary Options. These boundary options will identify all molecules in the structure regardless of whether or not they cross the formal unit-cell boundaries, and fill out a specified volume using simple translation or crystal faces or a sphere as boundary surfaces, these boundaries being applied to the centers of the molecules. Individual molecules can be identified with the cursor and highlighted or hidden completely (i.e. marked as non-plotting).

Atoms within molecules can be connected to each other with bonds or with polyhedra. Input bond specifications can be marked as inter-molecular, meaning that they will not be used in the molecule search.

Molecules located with these boundary options cannot be deleted, translated or rotated. Colors, etc. cannot be changed for molecules as a whole as opposed to individual input atoms. For these reasons, and because the molecule-locating algorithm is time consuming, it is often advantageous to use the Generated to Input conversion (Transform Menu). In this conversion, the symmetry and lattice translations are essentially lost, but the molecules can be optionally converted to fragments, which can then be duplicated, translated, rotated and deleted independently. Molecules which have been marked as non-plotting may be optionally deleted during the conversion.

2) Polymer groups

Many crystal structures have polymer units which are continuously bonded in one, two or even three directions (lattice directions). It is often useful to be able to isolate these units, which requires a different approach from true molecules.

Polymer groups in crystals cannot be identified in the Molecules in Crystal Boundary options because the bonding is continuous. To deal with such groups, it is first necessary to define boundaries for the drawing using one of the boundary options which apply to individual atoms, not molecules. Then bonded groups can be located individually in either of two ways: with the Find button in the Generated Atom Data dialog which comes up when you click on an atom in the display; or with the Locate Groups option in the Transform menu. In either case the units identified are limited to the current generated atoms, i.e. those within the current boundaries, whereas the special boundary options in 1) above locate complete molecules regardless of the boundaries. That is to say, in 2) groups may be truncated (which is necessary in the case of polymers) whereas in 1) molecules always maintain their integrity.

Groups identified in this way are not permanent - the groupings disappear when the structure is saved in a file, although if some groups have been hidden, the individual atom numbers will be saved in the list of non-plotting atoms. Having made the desired identification of groups, it may thus be advantageous to use the Generated to Input conversion (Transform Menu), converting groups to fragments which are then saved in the data (.str) file.

3) Structure fragments

ATOMS can combine portions of completely separate crystals and/or molecules (termed fragments). This is most commonly used for epitaxy (crystal on crystal or molecule on crystal), but can also be used for combining molecules, for example to depict chemical reactions. These fragments can be duplicated, translated, rotated and deleted independently.

Fragments can exist only in the Input=Generated boundary/operating mode, which is attained only by going through the Generated to Input transformation (Transform Menu). As explained above, molecules or polymer groups can be converted to fragments, so fragments can represent 1) molecules, as identified with one of the Molecules in Crystal boundary options; 2) polymer (or molecular) groups, as identified with the Find button in the Generated Atom Data dialog (after clicking on an atom) or with the Locate Groups option in the Transform menu; 3) completely distinct structures, obtained by reading from files or by one of the other options in the Multiple Structures options in the Transform menu.

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It is not possible to identify groups or molecules when in the Input=Generated mode and more than one fragment is present. However, all the atoms can be combined into one fragment with the Consolidate option in the Locate Groups dialog (Transform Menu), and you can then start over with identification of molecules or groups. Of course all molecules or groups will have to be identified individually.

Molecules, groups and fragments do not have to contain more than one atom, nor do they have to be electrically neutral. Furthermore, the atoms of fragments are not necessarily connected by bonding. For example, in structures with cations and anion radicals, for example CaCO3, using the Molecules in Crystal boundary options will result in each Ca atom, as well as each CaCO3 group, being identified as a molecule. The Generated to Input transformation would (optionally) convert each of these molecules to a fragment. On the other hand, if you calculate a CaCO3 crystal using one of the boundary options for individual atoms, then identify each CO3 group (but not Ca atoms) and finally use the Generated to Input transformation, all the Ca atoms will be grouped in one fragment.