The majority of tasks required for the refinement of a macromolecular model can be performed by TNT's shell commands. These commands are defined as aliases in the script $tntbin/logicals, which should be ``sourced" every time you log in.
TNT's commands are listed in Table 
. The main commands
for refinement are bf tnt and cleanup. tnt does the actual refinement
while cleanup is used to remove temporary files if refinement is interrupted.
The rest of the commands are used to check agreement of the model to the restraints,
work with noncrystallographic symmetry, produce data files for your model building
program, and to generate TNT format files from what you have. Each command is
described below.
Table: TNT Refinement Commands