Dialog Box - called from: Input1 Menu
For crystals and polymers, some limitations must be applied to the repetition of atoms by means of the lattice translations. Ten choices are available, as listed below. Note that the first three are not usually applicable to molecules, while the fourth, No Boundaries, is not applicable to crystals. There is an additional boundary option and operating mode, Input atoms = generated atoms, which is only accessible by choosing Generated to Input in the Transform menu.
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Options applied to individual atoms :
Default Unit Cell - Offers five sub-options to outline a volume with the same faces as the unit cell.
Enter Forms - Use specified crystal faces for the boundaries.
Slice - Isolate a slab of the structure parallel to a given face, with thickness equal to the d-spacing (or multiple thereof).
No Boundaries (molecule) - Use no boundaries at all. This option is primarily for a single molecule not in a crystal structure, not isolation of molecules in a crystal structure (see below).
Translation Limits (polymer) - Use integral numbers of unit cells.
Sphere - Include all atoms within a given distance of a given point (or atom).
The Unit Cell and Slice options always use lattice translations in all three axis directions, and the No Boundaries option never uses lattice translations. The Translation Limits option, primarily intended for polymers, allows you to specify which axis directions use lattice translations. The Enter Forms option also allows disabling of any of the lattice translations.
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Options applied to groups of atoms (molecules) in crystals.
In all these options, molecules or other bonded groups within the unit cell are located, and the center point of each group is found by taking a non-weighted average of the atomic positions. Then the selected boundary method is applied to these molecular centers.
Atoms within molecules or groups must be connected by Bonds or Polyhedra, and there must be no standard bonds or polyhedra connecting atoms of different molecules. However, bonds can be specified as inter-molecular, so that they will not be used in the molecule-locating algorithm but will be displayed.
Note that these options are not applicable to 1- and 2-dimensionally continuous groups (polymers) - bonding must be discontinuous in all three lattice directions. In order to isolate polymers, it is necessary to first use one of the six options above, then click on an atom in the polymer and use the Find button in the Generated Atom Data dialog, or use the Locate Groups option in the Transform menu. See Dealing with Molecules, Groups and Fragments for more information about handling groups of atoms.
Unit Cells - Molecules - This will find any and all symmetry-unique bonded groups, and can also show groups in additional unit cells. This option starts with a seed atom inside the unit cell and finds all atoms bonded to it including those outside the central unit cell - thus the bulk of a molecule may be outside the unit cell.
The other options below are actually identical to the options of the same name above, except that they are applied to the centers of molecules instead of individual atoms. The center, which is the average of all atoms in the molecule, is always within the given boundaries (this is not guaranteed in the Unit Cells - Molecules option).
Enter Forms - Molecules - Use specified crystal faces for the boundaries.
Slice - Molecules - Isolate a slab of the structure parallel to a given face, with thickness equal to the d-spacing (or multiple thereof).
Sphere - Molecules - Include all molecules within a given distance of a given point (or atom).