Dialog Box - called from: Import File, Bond Data dialog
This will derive a set of bond specifications for the atoms currently in memory, which may have just been read in from an import file.
Source of atomic radii. Starting with V4.0, ATOMS can use a constant set of radii in an internal table (read in from the RADII file), rather than the given input atom radii (which is still an option). If you choose to use the table, the element can be identified either using the first two characters of the label, or using the type number which is assumed to be the atomic number. If you choose to use the input atom radii, the atom list is scanned and the radius is taken from the first occurrence of each atom type. That is, if input atom number one is type 1 with a certain radius, and input atom number seven (for example) is also type 1 but with a different radius, only the radius of input atom number one will be used.
The Maximum distance as fraction of radii sum field specifies the upper distance limit for each type of bond. This will be the sum of the radii of the two atom types, multiplied by the number entered in this field. The minimum distance will be 0.2 Angstroms. If you choose to use the current input atom radii, the factor must take account of any reductions in the atomic radii from values which cause the atoms to almost touch.
If the Delete old bonds box is not checked, the new bond list will simply be added to the old list.
The All pairs/Cation-anion only radio buttons allows skipping many superfluous combinations, i.e. atoms which never bond with each other. In the RADII file, each atom is assigned a code indicating whether it is a cation (1), an anion (-1), non-metal (0) or inert (3). A "non-metal" is considered to be able to bond with all other types except inert atoms (rare gases). At the time of generating bonds, the codes for the two input atoms in question are added together, and any resulting values with absolute value greater than 1 are rejected. The codes in the RADII file are by default set up primarily for inorganic structures, and if you want to use this option for organic structures, they may need to be modified.
Whether or not this option is used, superfluous bonds can still be removed in the Bonds dialog in the Input1 menu.
In the Bond radii group of radio buttons, you can choose to make the bond radius a fraction of the radius of the smaller atom of the two in the bond; or to enter a constant radius for all bonds. A constant radius value of 0.0 will result in single-line bonds.
The Default Colors button will call up a dialog similar to that for individual input bonds (Bond Data ), but the atoms types, distance limits and radius will be missing.
If the Hydrogen bonds box is checked, a list of Specifications will be used to set up bonds for atoms involved in hydrogen bonding. This will result in two input bonds for each pair (H-other) which may be involved in hydrogen bonding. If the Hydrogen bonds box is not checked, any bonds involving hydrogen should be of the normal covalent type.