Section 25.2.4.4. Current structure of the package

TNT presents different faces to different users. Some users simply want to run refinement; they see the shell interface. Others want to use the TNT programs in untraditional ways; they see the program interface. A few users want to change the basic calculations of TNT; they see the library interface.

The shell interface is the view of TNT that most people see. It is the most recent structural addition, having been added in release 5E in 1995. At this level, the restraints, weights and parameters of the model are described in the `TNT control file' and the user performs particular calculations by giving commands at the shell prompt. For example, refinement is performed with the `tnt' command and maps are calculated for examination with some graphics program with the `make_maps' command. TNT is supplied with about two dozen shell commands. These commands allow the running of refinement, the conversion of the model to and from TNT's internal format, and the examination of the model to locate potential problem spots. The TNT Users' Guide describes the use of TNT at this level.

The program interface consists of the individual TNT programs along with their individual capabilities. TNT consists of the program Shift, which handles all the minimization calculations, a program for each module (restraints that fall into a common class, e.g. diffraction data, ideal stereochemistry and noncrystallographic symmetry) and a number of utility programs of which the most important member is the program Convert, which reads and writes coordinate files in many formats. The user can write shell scripts (or modify those supplied with TNT) to perform a great many tasks that cannot be accessed with the standard set of scripts. The TNT Reference Manual describes the operation of each program.

If the programs in TNT do not perform the calculation wanted, the source code can be modified. The source code to TNT is supplied with the standard distribution. In order to make the code more manageable and understandable, it is divided into half a dozen libraries. All TNT programs use the lowest-level library to ensure consistency of the `look and feel' and use the basic data structures for storage of the model's parameters and the vital crystal data. To add new functionality, one can either modify an existing program, write a new program using the TNT libraries as a start, or write a new program from scratch ignoring the TNT libraries. As long as a program can read and write files of the same format as the rest of TNT, it will work well with TNT, even if it does not share any code. A library exists, but is not copyrighted, that contains subroutines to read and write the crystallographic file formats used by the rest of TNT.