This option will locate all symmetry-unique bonded groups, or all bonded groups, within an integral number of unit cells. The central-ligand bonds in Polyhedra are used as well as the standard Bonds. Like the Locate Groups option (Transform menu), this boundary option starts with a seed atom, in this case the first input atom, which is within the zero or central unit cell (fractional coordinates 0.0 to 0.9999) and then finds all others involved. If the first molecule found in this way does not include all input atoms, the excluded input atoms are in turn used as seed atoms, until all are located. An alert informs you if there is more than one molecule or group. While the seed atoms are always in the central unit cell, any other atoms may be in adjacent unit cells.
If the number of atoms located exceeds the number in the unit cell the procedure is aborted. In such a case there is presumably continuous bonding.
You can locate all molecules in the unit cell, or only symmetry-unique ones. You can also show the molecules in multiple unit cells. In this option, the boundaries of unit cells are always the planes at fractional coordinates 0.0, 1.0, etc. To have more control over boundaries you can use the Enter Forms - Molecules boundary option. Note that that option finds the center of each molecule (unweighted average of atom locations), and then places molecules within boundary faces according to that center location, whereas this option does not find the center of each molecule, and molecules may be placed "inside" the unit cell even if only one atom (the seed atom) is actually inside the cell.
After initial isolation of the molecules, it may be desirable to use the Generated to Input conversion (Transform menu). This will simply make a list of the atoms located, which is saved in the data file, and will in the future avoid the molecule-locating algorithm, which can be time-consuming.
Do not use this option to isolate two- and three-dimensional polymer units. Instead, use some other boundary option to generate a volume which you know includes a sufficiently large number of polymer units. Then use the Locate Groups option in the Transform menu - this option allows the specification of particular seed atoms. The Locate Groups option is also appropriate if there are isolated molecules as well as a continuously bonded framework, or polymers. See also Dealing with Molecules, Groups and Fragments.
This is a possible default boundary option for importing crystal-data files, with certain exceptions (PDB, CCDC-FDAT, VIBRAT). If it is allowed, the initial dialog for that import file type will give a choice between Locate Molecules in Crystal and Default Unit Cell. Of course the boundary option can be changed after the import file is read in.
In the case of CCDC FDAT files, the "molecule" option does not use this boundary option, rather it uses data on molecules which is already present in the file.