A series of refinement cycles is executed with the tnt command. This command centralizes all the steps which are common to all refinement cycles. It reads the file init.cor and produces a file named cycX.cor, where X is the cycle number, for each cycle. When the cycles are complete a new init.cor is created which contains the most recent coordinates.
The first two parameters are required. They simply provide the starting and ending cycle numbers. The default <method> is `pcg' which indicates the Preconditioned Conjugate Gradient method (also known as the Conjugate Direction method). When performing rigid body refinement one must use the Steepest Descent method, indicated by `sd'. The fourth parameter allows you to define an alternative refinement script. For example, if you wish to restraint noncrystallographic symmetry you should specify the script $tntbin/tnt_cycle_ncs .
You may try out the tnt command by running some refinement on one of the supplied examples. Change your directory to $refroot/tnt/doc/examples/phrm. Copy the initial coordinate model, add_b_phrm.cor, to init.cor. Then type ``tnt 1 30 | tee test.log''.
The first cycle will be called number 1 and the last cycle to run will be 30. Compare the contents of test.log with standard.log to verify the correct operation of TNT.