One can enter either a set of Fourier coefficients or a map and request that Fourier list the peaks in that map. Fourier will locate each peak and attempt to deduce the parameters of an atom which would generate a peak of that height. Fourier will always produce an atom with an occupancy of 1.0. The temperature factor will be chosen to replicate the height of the peak in the map. The position of the peak will be the nearest grid point. If possible Fourier will produce atoms of type ``O". If the temperature factor of an oxygen atom must be below 1.0 to generate a peak of the needed height heaver atom types will be tried.
The default region of space for difference map peaks is a molecular volume. Of the many possible symmetry images of a peak, one is chosen which is closest to an atom in the current coordinate set. If Fourier has been given no coordinates the peaks will be placed in the real-space asymmetric unit. The peaks in a arbitrary region of space can be selected using the GRID and LAYOUT modifiers of the PUNCH command.
When PUNCHing peaks the additional modifier `HIGHEST' is available. In the default case all peaks in the map are listed to the output file. One can use the HIGHEST modifier to ask that only the tallest peaks are produced. The number following the word HIGHEST is the number of peaks to list.
The conversion from peak height to temperature factor is very sensitive to errors in the scaling of the observed and calculated data, as well as to the presence of the low resolution components of the map. A high resolution refined difference map which includes all the low resolution data will provide good estimates of the temperature factors of the atoms identified. As the map becomes poorer the estimates will develop greater errors. The tendency will be to overestimate the magnitude of the B factor.
Most people do not realize it but the scale of a Fo-Fc map is different
that that of a 2Fo-Fc map. A Fo-Fc map must always be multiplied by
a factor of two to be placed on an absolute scale of electrons/Å 
.
If you have a refined model and choose one water molecule to study you
may find, for example, that the density at the center of the atom in
a model map is 2.5 electrons/Å . If you remove the atom from the
coordinate file and calculate a Fo-Fc map you will find the peak height
is only 1.25.
(This is exemplified in the derivation of the 2Fo-Fc map coefficients.
One starts with a Fc map. Next a difference map (Fo-Fc) is added but
because the Fo-Fc map is on a different scale it must be multiplied by
two before the addition. The result is Fc + 2(Fo-Fc) or 2Fo-Fc.)
In almost all uses of the peak pick function the input
coefficients will be difference coefficients, and they will have to
be multiplied by two. This operation is performed using the SCALE modifier
on the FILE statement which introduces the map or coefficient file. The
example below (way below!) may make this issue more clear.
Example of the Calculation of Structure Factors in P6 
This example will convert a list of coordinates to a set of Fourier coefficients.
$tntbin/fourier << $eof CELL 111.9 111.9 98.2 90 90 120 RESOLUTION 20 2.5 INCLUDE $tntdata/symmetry/p63.dat INCLUDE $tntdata/formfactor.dat INCLUDE init.cor PUNCH testfc.hkl HKL $eof if ($status >< 0) then exit 1
To calculate a model electron density map instead the PUNCH command in the the example should be replaced with
This command will write to the file test.map an asymmetric unit of electron
density with a blur of 20Å 
. The sampling rate will be chosen to be the
coarsest allowed for this blur.
Converting an HKL File to a PACKED File
This example converts a data set from HKL format to PACKED format. Because there is no data type conversion the cell constants and symmetry operators are not required.
$tntbin/fourier << $eof FILE MIRPHASE bcl.hkl FORMAT HKL PUNCH mir.pak PACKED SOURCE MIRPHASE $eof if ($status >< 0) then exit 1
Converting a MAP File to an HKL File
This example converts a data set from MAP format to HKL format. An asymmetric unit of map must be supplied in density.map.
$tntbin/fourier << $eof CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 1.7 INCLUDE $tntdata/symmetry/p6122.dat FILE MAP density.map FORMAT MAP PUNCH coefficient.hkl HKL SOURCE MAP $eof if ($status >< 0) then exit 1
Converting a PACKED File to a DSN6 Map File
This example will convert a set of Fourier coefficients to DSN6 map format. The coefficients are in the file 2fo-fc.pak. The coordinate file current.cor is read simply to allow the layout of the DSN6 map to be determined by the model's molecular volume.
$tntbin/fourier << $eof CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 1.7 INCLUDE current.cor INCLUDE $tntdata/symmetry/p6122.dat FILE COEFS 2fo-fc.pak FORMAT PACKED PUNCH 2fo-fc.dsn6 DSN6 SOURCE COEFS OVERSAMPLE 4 $eof if ($status >< 0) then exit 1
Locating the Peaks in a Map
This example locates the peaks in a difference map. Because map files are so large it is inefficient to read and write them. It is always better to use the PACKED Fourier coefficient file format to transfer the information instead. Here the difference coefficients are to be found in the file fo-fc.pak and the current model is located in current.cor The 30 tallest peaks are written to peaks.cor.
$tntbin/fourier << $eof CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 20 1.7 INCLUDE current.cor INCLUDE $tntdata/symmetry/p6122.dat INCLUDE $tntdata/formfactor.dat FILE FO-FC fo-fc.pak FORMAT PACKED SCALE 2.0 PUNCH peaks.cor ATOMC SOURCE FO-FC HIGHEST 30 $eof if ($status >< 0) then exit 1
Adding Two MAP Files
The new file is created by adding map_1.map and map_2.map.
$tntbin/fourier << $eof FILE FIRST_MAP map_1.map FORMAT MAP FILE SECOND_MAP map_2.map FORMAT MAP PUNCH new.map MAP ADD FIRST_MAP SECOND_MAP $eof if ($status >< 0) then exit 1
Note the the adding of two maps does not require that you enter the space groups of either map. However you should be aware that the resulting map will have the space group that is the greatest common subgroup of the space groups of the two arguments. If you ask for the Fourier coefficients of the result of the summation TNT will use the proper space group in the calculation.
Correcting the Asymmetric Unit of Coefficients
$tntbin/fourier << $eof CELL 94.1 94.1 131.4 90 90 120 RESOLUTION 1.5 INCLUDE $tntdata/symmetry/p6122.dat FILE FOBS bad_asymm.hkl FORMAT HKL PUNCH good_asymm.hkl HKL CORRECT FOBS $eof if ($status >< 0) then exit 1
This example (which is basically the code for the shell command correct) moves the data from the file bad_asymm.hkl to the correct asymmetric unit, removes all redundant reflections, notes all inconsistent duplicate reflections, sorts the remaining ones into the desired order, and writes the resulting data set to good_asymm.hkl.
REPORT {FILE <Id> | SPACEGROUP}
The REPORT FILE command instructs the program to list interesting things about a map or coefficient file on disk. Among other things, it will list the r.m.s. value for a map file or the r.m.s. value for the map which would result from a file of coefficients. The program will also list the Wilson B factor for a coefficient file. The calculation of the Wilson B requires the scattering factors for the atom types present in the model.
$tntbin/fourier << $eof CELL 94.1 94.1 131.4 90 90 120 INCLUDE $tntdata/symmetry/p6122.dat RESOLUTION 1.5 INCLUDE $tntdata/formfactor.dat FILE FOBS pgn.hkl FORMAT HKL REPORT FILE FOBS $eof if ($status >< 0) then exit 1
For Fourier coefficient files this report is accessed using the report_hkl shell script.
The REPORT SPACEGROUP command causes Fourier to write its analysis of the current space group. It lists the equivalent positions, the lattice class, the point group symmetry, and the centric zones.
$tntbin/fourier << $eof INCLUDE $tntdata/symmetry/p6122.dat REPORT SPACEGROUP $eof if ($status >< 0) then exit 1