Command Statements

Command Statements

These statements cause Geometry to perform a particular action using the data that has already been entered on other statements. Most of the examples INCLUDE the file $tntdata/tntgeo_v010.dat. This file contains the full set of standard geometry for TNT.

In addition your control file, presumed here to be named your.tnt, must include the CELL statement, space group definition, sequence file, and your weights. In addition, your control file must also defined the standard geometry for any unusual groups in your model.

CURVATURE <File name>

This command is used in the long loop of refinement. It causes the function value, and the first and second derivatives of the geometry restraints to be calculated and written to the file specified. This command must be preceded by at least the geometry definition, a coordinate set, the space group, and a WEIGHT statement.

$tntbin/geometry << $eof
INCLUDE $tntdata/tntgeo_v010.dat
INCLUDE your.tnt
INCLUDE init.cor
CURVATURE geometry.dat
$eof
if ($status >< 0) then exit 1

FUNCTION  <File name>

This command is used in the short loops of refinement. It causes only the function value for the geometry restraints to be calculated and written to the file specified. This command must be preceded by at least the geometry definition, a coordinate set, the space group, and a WEIGHT statement.

$tntbin/geometry << $eof
INCLUDE $tntdata/tntgeo_v010.dat
INCLUDE your.tnt
INCLUDE shifted.cor
FUNCTION  geometry.dat
$eof
if ($status >< 0) then exit 1

GRADIENT <File name>

This command is used in the long loop of refinement when the method of minimization is to be either steepest descent or conjugate gradient. It causes the function value and gradient for the geometric restraints to be calculated and written to the specified file. This command must be preceded by at least the geometry definition, a coordinate set, the space group, and a WEIGHT statement.

$tntbin/geometry << $eof
INCLUDE $tntdata/tntgeo_v010.dat
INCLUDE your.tnt
INCLUDE init.cor
GRADIENT geometry.dat
$eof
if ($status >< 0) then exit 1

REPORT {GEOMETRY | STRUCTURE | SYMMETRY}

There are three different report types listed below.

• GEOMETRY

  This command causes the printing of the geometry statistics on a per geometry restraint basis. For each restraint entered in the geometry library the mean and r.m.s. deviation from the standard value of the occurrences of that restraint will be listed. For example, this listing would contain the average and r.m.s. deviation for the CA, CB bond length in all ALA residues in the structure. This listing is useful when looking for systematic deviations from the standard value of a geometry restraint in the library.

• STRUCTURE

  This command causes the printing of a list of a small number of interesting things about a structure. If a CELL statement has been given the cell constants will be echoed along with the reciprocal cell constants and the orthogonalization and deorthogonalization matrixes. If atomic coordinates have been given the number of atoms will be listed along with the number of residues in the structure. In addition the location and extent of each chain will be printed.

• SYMMETRY

  This command causes the printing of a list of the symmetry operators that have been entered. Each symmetry matrix is printed in crystallographic coordinates with the translation vectors added so that when a symmetry operator is applied to a molecule a nearest neighbor molecule is generated. Each operator is listed with the name that the SCREEN listing uses to refer to that operator when a bad contact is found between atoms of two symmetry related molecules.

SCREEN <Number>

This command is used to get a list of the worst so many bonds, angles, etc.. It requires that the geometry library, space group, and a coordinate set be given.

$tntbin/geometry << $eof
INCLUDE $tntdata/tntgeo_v010.dat
INCLUDE your.tnt
INCLUDE shifted.cor
SCREEN  20
$eof
if ($status >< 0) then exit 1