This program is quite simple to run. All you have to do is provide the information from each module, and describe any modifications to the shifts you wish to make. The most common type of refinement uses the crystallographic and stereochemistry modules. Usually we do not have high enough resolution to determine the occupancies of the atoms in the molecule. The occupancies will have to be held fixed. The data the program needs in the long loop is:
$tntbin/shift << $eof INCLUDE geometry.dat INCLUDE rfactor.dat INCLUDE init.cor INCLUDE olddir.dat CONSTANT OCC $eof if ($status >< 0) then exit 1
Usually the CONSTANT, COMBINE, and other parameter editing statements are placed in the TNT control file. The CONSTANT statement here is placed in the script for illustrative purposes only.
The information from each module is contained in rfactor.dat and geometry.dat. These files must contain, at least, the function value and gradient of their respective terms. If the files also contain the curvature Shift will be able to use the more powerful methods of function minimization.
The initial coordinates are contained in the file init.cor. The shift vector, or direction file, is contained in olddir.dat. This file is the shift applied in the last cycle. During the first cycle of a series there will not be an olddir.dat, therefore you should ensure that an empty one exists. Its presence will keep Shift from reporting a ``file not found'' error message.
The occupancies of all atoms are held fixed. Because this is the only CONSTANT statement all the positions and temperature factors will be varied.
The input to SHIFT during a short loop in this same cycle looks like:
$tntbin/shift << $eof INCLUDE stpfil.dat INCLUDE newdir.dat INCLUDE init.cor INCLUDE geometry.dat INCLUDE rfactor.dat $eof if ($status >< 0) then exit 1
Note that stpfil.dat and newdir.dat are now included. stpfil.dat contains the history of this cycle while newdir.dat contains the current shift vector. olddir.dat is no longer needed. It should be deleted at the end of the long loop.
Again init.cor is read. Shift will always work relative to the initial coordinates.
The TNT control file is not required in the short loops.
Information from the individual modules is again passed in geometry.dat and rfactor.dat. However in the short loops these files need only contain the function values.
The CONSTANT statements should not be reentered in the short loops because the knowledge that they had been entered in the long loop has been stored in newdir.dat.