Often one will encounter a side chain for which the density is a superposition of two different conformations. It is quite easy in TNT to model these side chains. When there are alternative locations for a particular atom the different possibilities are marked by adding a code to the end of the atom's name with a period between the original name and the code.
This sounds more complicated than it is. An example will make the point more clear. Let us say that the distal three atoms of an ASP amino acid occurs in three conformations. We will use the letter A to indicate the first, with B and C indicating the other two. The names of the three atoms are CG, OD1, and OD2. Therefore the names of the disordered atoms become CG.A, CG.B, CG.C, OD1.A, OD1.B, OD1.C, OD2.A, OD2.B, and OD2.C.
TNT will automatically recognize that this side chain is disordered and appropriately apply the stereochemistry restraints for an aspartic acid.
It is very important that you do not use an atom name with a disorder indicator along with the same atom name without one. If OD1 is disordered in a particular residue there can be no atom named, simply, OD1. If any versions of an atom are marked by a letter they all must be.
When one considers stereochemical interactions between residues it is presumed that atoms marked with .A will interact with other atoms marked .A but not with atoms marked with other letters. If the atoms 123:OD1.A and 132:NH1.A are too close together they will be pushed apart because of the bad contact. However 123:OD1.A and 132:NH1.B can be superimposed and the contact will still not be considered to be bad.
In addition, if residues 123 and 124 are linked in the sequence file by a PEPTIDE bond and each are entirely disordered, the .A version of 123 will be considered to be connected to the .A version of 124 and the .B versions of 123 will link to the .B version of 124. Again no bad contacts will be refined between the .A's and .B's.