A difference map is usually some function of both Fo and Fc. Since scaling of the two structure factor sets is required you need to use the program Rfactor. If all you want is a 2Fo-Fc or Fo-Fc map you can use the make_maps shell command. If you want some other map you should take the script $tntbin/make_maps and edit a copy to change the type of the Fourier coefficients to those you want.
Rfactor has the capability to produce difference maps of many different types. These types are listed in a table in the TNT Manual.
Fourier transforms are calculated with the program Fourier. If you want to calculate a map from coefficients simply PUNCH a map using the coefficient file as the "source". If you want the other direction PUNCH the coefficient file with a map file as its source.Usually Fourier transforms do not need to be explicitly calculated in TNT. Any operation that requires crystallographic data will accept either a map or a set of coefficients as input. As coefficient files are smaller you should try to store data in that form whenever possible.
The only map file formats supported in TNT are the traditional Ten Eyck map format and Alwyn Jones' DSN6 map format. TNT will not read a DSN6 format file. This means that the only conversion possible is to convert a Ten Eyck map file to DSN6. This is done with the program Fourier. Simply PUNCH the DSN6 format map using the Ten Eyck map as the "source". Such conversions are usually unnesesary because any TNT program that can write a Ten Eyck map file can write a DSN6 file directly.
An example script for this format conversion is
>$tntbin/fourier include my.tnt file map_file current.map format map punch current.dsn6 dsn6 source map_file >
This script converts the map file named current.map to the DSN6 format map current.dsn6. The TNT control file, here called "my.tnt", must be INCLUDEd because a DSN6 format file contains the cell constants but a Ten Eyck file does not.
To read or write PDB or DSN2 format coordinate files use the from_pdb, from_dsn2, to_pdb, or to_dsn2 shell commands. For other file formats you need to write a script for the program Convert. You can use one of those scripts supplied in TNT as a template. Remember, one usually cannot convert file formats without some manual editing.
The program Convert can produce TNT coordinate files from Bob Diamond's (RDI or DIA extensions) and Wayne Hendrickson's (ATM or WAH extensions) coordinate file formats in addition to Alwyn Jones' DSN2 format and the Brookhaven Protein Databank's PDB format. In addition to all these formats it can read the ancient AMSOM format.