The method of standard geometry definition used in TNT is very easy to understand and to modify. There are eight geometrical relationships which can be set to ideal values for a standard group -- bond length, bond angle, torsion angle, pseudorotation within 5 membered rings, planarity around trigonal atoms, general planarity, B factor correlation, and chirality of an atom. Chirality is included only to warn the user when a group has the wrong handedness; it is not considered a restraint and does not affect the shifts of the atoms.
Geometry restraints are defined for each type of residue and each type of link between residues. For example, there are geometry restraints associated with the residue type THR (threonine). These would include the bond length between the atoms CB and OG1. Other restraints are associated with the PEPTIDE link. These include the bond length between the atom C of the previous residue and the atom N of the following residue.
Defining the standard geometry of a molecule consists of simply defining the geometric restraints for each residue type and linkage type in your model. Most of this work has been done for you. The libraries distributed with TNT are described on page . If you have something unusual in your model you should read the example on page .
One of the best things about TNT is that a prosthetic group, such as a heme molecule, is treated just like any other standard group. It is very simple to define the standard values for such groups. In addition, atoms for which there are no restraints such as metal ions or water molecules, do not appear in the geometry declarations at all.