TNT is supplied with scripts for performing the most common types of refinement. These scripts are listed in Table .
Table: Scripts Supplied with TNT.
The simplest means to develop a new script is to modify one of these files. To understand the data flow within a TNT refinement job you must understand the file naming convention and the way the different terms in the equation are implemented in the programs of TNT.
The input to a cycle of refinement is the starting model, named by convention init.cor, and the optional old shift vector named olddir.dat. Because the results of each cycle is usually fed into the next the output of a cycle of refinement is the same type of data -- a coordinate file and a shift vector. However the new files have different names: shifted.cor and newdir.dat. The code provided by these scripts renames shifted.cor to init.cor and newdir.dat to olddir.dat at the end of each cycle.